To avoid an essay, I'll give my ideas hard and fast:
1) Mod combo I liked: Terran Plasma Weapons + Elerium breakdown Mod:
Why: Once you research alien plasma weapons your workshop is really nothing more than an Avenger factory. Terran Plasma weapons forces me to build my own plasma weapons and ammo--this made some missions REALLY tense as my operatives ran out of ammo and couldn't just mug a Muton for his gun. The elerium breakdown mod made this one bearable as I could deconstruct alien artifacts to get 25-75% (based on mod parameters) of the item's elerium construction cost.
2) Mod Combo I liked: Alloy Craft (Retaliator and Sky Marshall):
Why: These two "in-between" craft made so much sense to me, and were VERY practical: After alien alloy research XCOM makes its own improved Interceptor and Transport based on existing designs. Each is improved (better speed, range, and HP with Interceptor, Skymarshall actually had more carrying capacity). And, lore-wise, XCOM would logically have to master human craft and alien technology integration BEFORE moving on to reverse engineering UFOs. And Elerium-wise it was nice to have somewhat improved jet-fuel using craft (that didn't have a rental fee for the Retaliator--I edited the Skymarshall to also not require a rental fee).
3) Mod I Like: Alien Alloy Ammo + Mod Suggestion: Alien Alloy Weaponry:
Why: I liked the alien alloy mod lore-wise as it was XCOM's baby-steps into alien technology--trying to force alien ideas into a human template. I like the idea of a pre-laser alien alloy ammo weapon as a stepping stone for the same reason. Plus, if done right I think alien alloy weapons could be a laser weapon alternative or complement: Lasers have unlimited ammo, whereas alloy weapons would take ammo but do more damage (or something).
4) Mass Accelerator Weapons + My own personal Armor mods:
Why: I liked this combo because I think it encapsulates the spirit of the XCOM story. The Mass Accelerator weapons are BETTER than alien plasma, and my personal armor mods gave soldiers the protection and stat boosts to stand toe-to-toe with Mutons.
How does this combo capture the XCOM spirit? The aliens have been using the same technology for millions of years in a unified, slavish existence under a single hive-mind. Humans are different. We're divided into a council of funding nations. We adapt. We change and grow. And we improve the living @#$% out of the alien technology until
WE SEND E.T. HOME--IN A BODY BAG! 
5) Mod I like: PSIONIC ARMOR:
Why: A mod of a mod, someone took the purple power armor recolor, reduced the stat protection (to around personal armor!) but added psionic resistance to make the wearer impervious to mind control. This made my cannon fodder troops useful as they wouldn't be MC'd, but more vulnerable than 70+ psionic strength operatives in regular armor. Was it worth the elerium to have that 60 accuracy new recruit? Very very tense scenarios.
6) Suggestion: Research Guidance
Why: When I got XCOM nearly 20 years ago it was odd to me that I needed to buy a strategy guide or a PC Gamer mag to figure out the research order. I would suggest that research items have XCOM scientist suggestions as to your next course of action.
EXAMPLES:
"We will need to capture and interrogate an ALIEN LEADER if we want to discover more about ALIEN PSIONICS.*
"We should take possession of a UFO POWER SOURCE and research it to derive more advanced XCOM craft."
Good luck with your mod!
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