I'm about to complete my first game-year, and just found an alien base. Deciding whether or not I can take it out. Best armor I have is chainmail or tactical armor, doing pretty well on weapon collection/research, so I think my firepower is in decent shape. Although, I did run from some mercenaries, figured they were too much for me (but I made their craft take off).
Dojos are best to slow-drip improvements to units in other bases besides your main. Like lokknars, peasants, all those spare young-ubers that pop up and recruited raider scouts.
Ill make this simple for you about Enemy Bases. Send in an attack to find out which faction is there, then reload your Geo save. Now you know how screwed you might be.
Church - Doable
Academy - Doable but watch out for cyberdisks
Traders - You're screwed, you'll never take down the big boss. Need Rail Driver.
Mercs - You're screwed until late game, and even then you're not walking out without a limp.
(... though a cursory assault on Supply Ships or Hyperwave detection will tell you who's there)
Generally speaking you need to bring your Lasguns and fight defensively. Someone needs iGuns or Gothic Rayguns to help with anyone who might have shields. You can win but in year2 its mainly the Melee gals who will rack up corpses. And melee needs to have at least 100 TUs.
By defensive fighting I Mean It. Those 20x20 rooms will butcher you, whether directly or due to line of fire down the halls.
If you have a Syn Gal (android lady) give her chiller armor with the attack claws on it - she's the one you want to send into the command center to take it down. Because of her insane TUs and reactions/melee and damage resistance. She can get past the several dudes who will be in the wraparound hallway to reach it. Then she only needs to deal with maybe 1-2 mobs in the control room and entrance itself.
Should be possible by mid year 2 to have Death Blossom (big smg pistol thing) and usually thats how I roll with it. Basically a one handed Boarding Gun with lots of shots.