In a way, yes, everyone having exactly the same weapon is a bit dull...
However, having to mix all weapons is also tedious - you have to make sure every group of people you send out has at least one laser, one tachyon, one bullet-based, explosive, plasma... you can't split your 8-man team into two any more, because there's a good chance one of your teams will run into something it doesn't have the weapons to handle.
The alternative is to send all of your people around in one big group, so that the weapon you need to deal with a specific alien is never far away. Disadvantage: When the aliens land some high explosive in the middle of the group, it's not going to be good...
The game's pretty interesting in the beginning, anyway, even when everyone has basic weapons - you have a couple of assault rifles/pistols/SMGs, sniper, rocket launcher, shotgun and flamethrower - you don't have everyone carrying the assault rifle. Effectively, the troops could be armed with all one 'type' of weapon without everyone carrying around the exact same weapon.
There's also the issue of complexity - there is no chance I'm going to memorise which aliens are resistant to which technologies, and I don't want to be minimising the game and flicking through the manual to work out what to shoot the damned thing with...
I don't know... it seems sad to research a tachyon rifle, and then it's ineffective because the aliens on a certain mission are all resistant to it (but your old assault rifle you started off with would have worked perfectly).
Returning to an earlier point, two stage base assaults is a concept worth exploring - after all, it's likely the aliens wouldn't just allow you to walk into their base, and you'd have to land your Dropship outside and break in...
Maybe the development of stealth craft could skip the first stage...
-PsyW