Yeah, there's some valid points here. I think the most helpful thing to do is for me to fill you in on what I'm trying to achieve with the balancing, even if it doesn't necessarily map to what is currently in the game.
The basic idea is that the shape of the game is more like classic X-Com; in the early stages of the war your troops die in large numbers. You haven't developed the equipment to reliably protect your soldiers from alien weapons so many of the missions are a meatgrinder until the mid-game, where suddenly your soldiers will usually survive a shot or perhaps two before they keel over. Only a handful of your troops survived the opening stages of the war (more by luck than judgement) but they're now hardened badasses and your rookies now have a long enough lifespan to start levelling up. By the end of the game you've surpassed the aliens and only their elite units are much of a threat to you.
This doesn't work in the current version of X2 for a few reasons. The biggest reason is that the aliens are extremely accurate and deadly, but the starting squad is only 8 soldiers whereas in X-Com it's 14 soldiers so you can't absorb the losses like you could in X-Com. As well as adding the updated dropship, we're also going to be updating the starting dropship so it's got a larger troop capacity and has walls like the Skyranger did in X-Com and the Charlie did in X1. I'm not sure if we'll bump the starting team up to 10 or perhaps 12, as we're planning the advanced dropship to hold 15 (or maybe 16). Problem is, the tiles aren't ready for the updated starting dropship yet so we can't put it in the builds - maybe I'll add the blockout for it to an Experimental test build after we finish V6.3 though. That should make testing the balance easier.
Second thing is that the cover angles are too narrow, so there's very little you can do to protect yourself against those deadly aliens in terms of positioning (something we'll fix in an upcoming patch). Third thing is that I think in X-Com there's a much wider variety of aliens outside the UFOs, whereas in X2 the non-soldier aliens are only found inside the UFOs. This means for most of the mission you're fighting tougher aliens with better equipment. If we spawned some of the weaker aliens outside the UFOs then there would be more aliens that could be killed by a single rifle shot and carry weapons that might not instakill your troops at the start of the game. That'd probably be a sensible change.
The other thing to think about is what the individual races do:
Psyons - these are one of the two "easy" races you encounter in the early game, because psionic-capable Psyons don't appear for the first few weeks. After that it's generally fairly unwise to bring low-Bravery soldiers to battle against Psyons. Beyond their psionic abilities they're only standard combatants really, nothing exceptional.
Sebillians - these guys are the other "easy" race at the start of the game. I'll probably give them some kind of inherent resistance to energy weapons, which obviously only comes into play later in the game and makes them harder to deal with relative to other races. Depending on how we implement psionics these guys could be weak against psionic attacks.
Wraiths / Androns - these appear later in the game and are paired with Androns and Gun Drones. These guys are the most competent alien combatants, with high firing accuracy and reflexes, and Androns are resistant to kinetic weapons. However once you have energy weapons the combo becomes a bit less deadly.
Mantids / Reapers - I think we'll pair the Reapers with the Mantids, who are little spider-dudes. The Reapers are obviously extremely dangerous at melee range, whereas the Mantids use ranged weapons too. They're not tough but they are small units so they are harder to hit than normal, and are reasonably effective shooteres. I think in practice these guys will end up being fairly easy to fight, but there's an extra layer of danger any time Reapers are involved in a mission so it'll probably balance out.
Roughly speaking the Wraiths and Mantids start appearing when Corvettes and Fighters started appearing in X1. In the late game tougher Elite variants of each of the aliens start appearing.
Hopefully that gives you some kind of vague framework to work within?