asses vs assess: 'asses' is the standard plural of 'ass', which has been around since Old English, and pluralization doesn't change word stress. As the plural marker -es follows the stress, the vowel is reduced to schwa. 'assess' comes from Middle French 'assesser', which had stress on the end syllable. That got adopted into Middle English as 'assessen', with the -en being an infinitive ending (as it still is in German and Dutch). Removing that ending, as it would be when conjugated, you get the stem 'assess-', with stress on the end. Because that vowel is stressed, it isn't reduced to schwa.
these vs theses: 'these' goes back to Old English, and while the details aren't hugely important, suffice it to say that there were various processes that caused the /θ/ (<th>) and /s/ to become voiced as /δ/ and /z/. 'Theses' is from Ancient Greek (filtered through Latin), and is probably a relatively modern loan, vaguely from the Enlightenment if I had to guess. The Greek spelling is θέσεις (theseis). The Greek letter <θ> is strictly the voiceless 'th' sound (the sound in 'thing', NOT in 'this'). The first vowel is the 'bee' vowel /i/ because it's stressed, while the second one is also /i/ because that's how <ει> has been pronounced in Greek since vaguely the Roman era. English, like all European languages, has its own tradition of how to pronounce words from Greek and Latin that have diverged a fair bit from how they were originally pronounced, giving weirdness like this.
trough vs through: -ough is notoriously terrible, but it wasn't always this way. Back in Old English, these words ended in either -g or -h. -h was the ending sound of Scottish 'Loch', while -g was basically the same sound, but voiced. As you know, these sounds do not exist in English today, and so they generally either became silent or shifted to the next closest thing, often /f/. This depended on the exact phonetic context and was generally a mess, though I'll do my best to untangle things. 'trough' was 'trog' or 'troh' in Old English, while 'through' was 'thurh'. If I had to guess, I'd say that it went silent in 'thurh' because it was preceded by an /r/, and so it could be dropped while still being recognizable as the same word (note how you can easily still recognize the word didn't even if you don't pronounce the /t/). This wasn't the case in 'trog', and so it became an /f/ as the next closest sounding consonant. The 'loch' sound /x/ and /f/ both produce some raspy rush of air, so it's not completely weird.
though vs thought: this one is a bit messy. 'though' strictly speaking comes from Old English 'þēah', which we might expect to get an -f ending. However, it was conflated with Old Norse 'þó', which dropped the ending consonant and changed the vowel. A huge amount of Old Norse vocabulary entered English during the late Old English period and displaced quite a lot of native English vocabulary, including pronouns. 'them', for instance, isn't actually a native English word, but rather is from Old Norse. 'thought' comes from Old English 'þōht', where as before with 'thurh', the sound could be dropped without impeding word recognition. The evolution of the vowels is a whole hot mess due to English having one of the most complex vowel systems in the world, so I'm gonna just leave that as 'people talked and fucked the vowels up'.
though vs thorough: I don't think there's that much weird about this one? 'thorough' is from a corruption of Old English 'thurh' (through) into 'thuruh', which came to be used as an adjective and gained initial word stress that caused the vowels to evolve differently. It's not that goofy, all things considered.
thank god, we're done with the <gh> disaster. The Scots really had it right when they decided to just keep it.
stranger vs strangler: this is predictable. The <g> in 'stranger' is reduced to 'dʒ' (the consonant in "Joe") because it's followed by <e>, reflecting a stage of palatalization in Middle French where the word originates (originally Latin 'extraneus'). This isn't the case in 'strangler', so it behaves as normal. Oh, I guess the vowels are different; like I said, English vowels are a disaster. So, 'stranger' was borrowed from Anglo-Norman, a weird dialect of Old French originating from the Normans that conquered Britain. It was divergent from more standard Old French in a few ways, and in this case, 'stranger' comes from Anglo-Norman 'straungier'. This turned into a long /a/ in Middle English (the vowel of 'father'), which the Great Vowel Shift turned into vowel we have today. 'Strangle', on the other hand, comes from Old French 'estrangler' and entered English with a short vowel. So, 'strange' originally had a long /a/ while 'strangle' had a short /a/, and those both evolved into different sounds that are spelled with the same letter because English is insane.
gnome vs genome: 'gnome' isn't actually that old of a word. Some Swiss guy just made up the Latin word 'gnomus' in the 1500s. At that point, /gn/ either was already an invalid onset in English or was very soon to become so. 'Genome' was coined in the 1920s by a German guy, loosely based of a Greek word, so I would guess the stressed <e> was interpreted as if it were also Greek and thus pronounced /i/.
desert vs dessert: 'dessert' comes from Middle French 'dessert', itself from 'des-servir', literally 'dis-serve', as in removing what has been served in order to give you a tasty treat at the end of the meal. Because that initial 'des-' is a prefix, it wouldn't be stressed, thus we have stress on the end of the word. The first vowel may have been reduced to a schwa under continuing influence from French. As for 'desert', that comes from Old French, and while I would expect the ending to be stressed in French, it's entirely possible it was loaned early enough into English that English's native rule of stressing the first syllable took over. The later introduction of 'dessert' would have reinforced this.
moist vs maoist: Maoist is of course segmented as Mao-ist, and English doesn't have any way to clearly show that, so if Mo-ist was a real word, it would unfortunately also be spelled as 'moist'. Thankfully at least, 'ao' isn't a native English sequence, so that's a big clue, and 'aoi' is not a valid sequence for any single English sound. I think most languages would struggle with this sort of thing, since strong segmenting as happens with neologisms like this will happily defy standard phonological rules so long as speaker can recognize the segments and separate them accordingly.
flaming vs flamingo: It's a somewhat similar story here, with 'flaming' obviously being the application of -ing to 'flame'. 'Flamingo' is a loan from Portuguese, and English tends to not adapt loanwords to native phonology very much, but that's hardly unusual. Hell, in German, you also have 'Der Flamingo'. Funnily enough though, 'flamingo' is actually related to 'flame'; both come from Latin 'flamma', which entered English via Old French.
uniformed vs uninformed: Again, another segmentation issue, though it is a kinda fun one. Here, it's uni-formed and un-informed. Both do ultimately originate with Latin 'formare'. Here, the core thing is that 'inform' is a very common and easily recognized word, and we all know that the stress in on the ending. Adding another common prefix to it doesn't distract us from that, especially with the meanings being clearly related. 'Uniform', on the other hand, is much more liable to be analyzed as a single unit, since uni- is not a very common prefix and the connection in meaning to 'formed' isn't super transparent. So, we just treat is as a single largely independent word and that's that.
laughter vs slaughter: God damn it, you really had to bring <gh> hell back at the end. So as before, we get /f/ at the end of 'laugh' due to there not being any other consonant around to compensate for totally dropping the <gh>. Now, the obvious question is, why doesn't this apply to 'slaughter' as well? That's because 'slaughter' isn't actually a native English word at all. Again, we can blame our friends the Vikings for bringing 'slaughter' and literal slaughter to England. The Old Norse form was 'slahtr'. That first element, 'slah', is actually the same word as English 'slay'. So basically, there never existed an English word 'slaugh' that had that pronounced <gh>, and so to whatever extent it was pronounced in the Old Norse word, it could easily fade away without causing problems. Whereas for 'laughter', this is easily analyzable as 'laugh-ter', and since 'laugh' developed an -f ending, 'laughter' kept it in order to maintain consistency.
Truly, what a mess. Beyond sating some curiosity though, I hope this does go to show you that English really isn't total random chaos like it's often portrayed. Every apparent exception or weird spelling has a very real explanation behind it that tells a truly incredible story about an island that saw some Celts settle down, the arrival and then departure of the Romans, a violent conquest by the Anglo-Saxons, continued influence from Christianity, centuries of conflict with the Scandinavians, yet another conquest by the Normans, continuous cultural exchange with the rest of Europe, an explosion of Greek and Latin terms - many coined - during the Renaissance and Enlightenment, and then the modern age of globalization (and colonialism) that's resulted in the importation of words from all across the world. Every word is a story; you only have to take the time to read it.
(the English vowel system is actually insane though; I really cannot defend it lmao)
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