In general, rifles are a good skirmishing weapon, with decent close up damage but also the ability to reach out and hurt something further. In bases though, the distance over which you might need to reach something is severely limited so shotguns are generally better. You could use the soldiers who are usually snipers with rifles, so their retain their "sniper" role, but indoors sniper with more mobility and close range power with the autoshot.
Some HE is always good to have, it's kind of a FU card to play on the AI for many things. Cyberdisc gonna kill you, why not take him with you instead and kamikaze yourself with a high explosive. If you didn't use instant grenades, you could also throw it and retreat immediately around the corner, allowing your soldier to survive because the wall shields him from the explosion. You do need something to take care of cyberdiscs and it looks like rockets are not particularly good at it, on top of being rather difficult to move.
One thing I'm wondering though, having pretty much caught up on the LP, is why are you trying to assault Alien Base 2, which has floaters, reapers and cyberdiscs, when you could assault Alien Base 1 which only has floaters and reapers? That would get rid of the worst enemy, allow you to grab the tech and progress, then you could eventually go back in Alien Base 2 with more tech to kick their asses. Or did I misunderstand about the first base?
