The limited party size is only temporary. You'll soon be able to fight with a full party again (pretty much for the rest of the game, barring some cutscene-like fights at the end). The Yrana segment has a special mechanic full of (popular) cultural references. And the other two segments will introduce new party members. Soon after, you'll be able to mix and match.
I'll look into the problem with the skills, thanks for letting me know!
And the bats can be annoying at times, but you don't have to fight all of them. They're more like background objects that may occasionally run into you :)
Thanks once more for your useful insights, and I hope you at least had some fun while playing!