I disliked how the numbered hotkeys change for every unit. Overwatch would be on 2 on my heavy, but on 4 on my sniper. There was no consistency in them which was kinda bad.
The weapon tech tree was also limited in the sense that it was a linear progression. bullets < lasers < plasma. No reason to use lasers for long or to even buy more than 2 - 3 of anything. The armor tree was better thought out as towards the end each had their benefit. Titan for tanking, archangel for movement and increased mobility (though I used the flying ability maybe once), ghost for sneaky snipers/assaults and psi for increased psi-power.
The interception bit was also rather lackluster in regard to tech upgrades.
Avalanche < phoenix cannon < laser cannon < plasma cannon < emp cannon < fusion lance.
Once you get the the 1up, there's no use for the previous weapon. The game ramps up UFO difficulty a bit faster than you can level however, and at some point you're stuck to just abort interceptions until you get the firestorm. And then it's easy mode for a while again until the bigger baddies show up.
I like the game, but it could've been a bit deeper.