We've been playing a year and the better players always win regardless of what side they play. We've got every option available though, I've said it before, it's a lot harder (more expensive) to have a balanced bug force. E.g. To play an 'infantry' heavy large numbers force you need lots of warriors, to play a tank army, you need tankers, to play a shooting army you need plasmas and to play an aerial army you need hoppers and ripplers. For MI to be a shooting army, they need to put extra javelins in, to be an aerial army, you just buy everyone a capsule. You can upgrade to trench sweepers without altering models, you can give everyone a d10 attack by buying frag. The bugs don't have this luxury, you need different models to change the role of a force. When you've got them available, you can take on anything though.
Think about it, how many bug players have the luxury of 3 plasmas, 3 tankers a king and thorny tankers, 50 hoppers etc...... We set up armies as a group and we have got the resources. We find the game balanced because of it.
My favourite force is 100 workers and warriors, 2 brains and 8 hoppers. Absolutely lethal, go on attack and ignore the warrior casualties. If a unit of 10 can take out 3 cap troopers they are ahead on points
I don't think the MI are overpowered, but they are certainly a cheaper army to 'power up' and customise.
I think more upgrades for the warriors is what's needed, maybe specialist models that join the unit and pass on an ability? So you only need to buy one model to upgrade a unit. As it stands, the arachnids are always going to be expensive to buy. That means you compromise on what you get. Lots of warriors is a must, but a lot of players ditch them in favour of a tanker (due to the financial cost, not the points).
But honestly, a bug army with a lot of warriors and good use of tunnels is devastating. I usualy go workers and warriors, even if you lose most of them on the way, it only takes a couple to devastate an MI unit. And even the cheapest warrior has a D10 attack.
I also find winning with bugs a lot more satisfying.
Anyway, every group has it's complaints about over powered armies, it tends to be because a) a rule is being misunderstood or abused.
b) one player is just better than the rest and happens to use that army.
c) One player understands the rules better or has a better army because he's spent more
Another important factor in SST is the set up and tactics side of things, one mistake there can lost the game for you (our last game when my opponent selected second turn even though I had 3 plasma bugs... that was a brief game).
As for skinnies, yes they are tough, but really expensive, just fling warriors at them to keep them busy, then hopper the character models. Playing bugs is all about having so much cheap rubbish that it's not even worth him wasting the ammo