1) The Rock Band strum bar. Everyone seems to hate it. I really, really like it simply because it makes me feel like I'm plucking a string. It's squishy, and that turned me off at first. I'm used to pushing the strum bar with the pad of my thumb when I'm playing Guitar Hero because, well, it's a damned bar. So when I try pushing this squishy strum bar, my hand feels like it has to overcompensate because it's not giving back the "click" feedback. Al made this note to me when he had gotten the game, and at first I wasn't sure what he meant - but after I tried it, he was completely right and I understood after 60 seconds of playing a song.
So, I started "tapping" the strum bar with my thumb really lightly - and it worked, plus my hand didn't hurt. Problem is, I didn't feel confident that I was hitting all the notes - even though I was - because, again, there was a lack of feedback. However, I discovered that the extreme squish of the strum bar also meant that it was not prone to double-strumming if you flicked it really hard instead of pushing it down.
So, I started flicking the bar with the outer edge of my thumb (not the fleshy pad), as if I was plucking the string with my thumb. That quick "twang" of contact with the strum bar serves as great feedback, and it feels more like a string than a bar. Is this necessarily ideal for alt-strumming? No, but I'll live with that. It still feels great, again because the sensation is less like "push a bar" and more like "pluck a string."
2) Everyone seems to think the upper frets are too small. Everyone's probably right, but I don't really mind it because I like using them. I started out using them almost exclusively just because it felt cool to finally be able to rock out higher up on the fret board after three and a half (80's isn't a full game :P) games of staying at the neck. Aside from the occasional gaffe, I have no problem whatsoever with the size of the buttons. Tilting the guitar with my hand higher up the fret board lets me feel more in control of the fretting while holding the guitar at that angle. Since my left hand is now that much closer to the mass of the guitar, everything feels more balanced.
I've started playing up at the neck again, and getting used to switching back and forth so that I don't fumble for the buttons when I feel like switching between fret sets. Those huge ridges that bookend each set of frets are vital to this learning process; rather than release your hand and move it, hold it tight against the fretboard and slide it so that you can feel the ridge.
3) I've started to feel where the kick pedal might snap if drummers aren't careful. Take a look at the pedal - make note of where those ridges end near the bottom of the pedal as it tapers off. Put your heel at approximately that point. Now, press the kick pedal in fully. After this, ever so carefully, apply more pressure with just your heel. You may feel the pedal "bending" there. This freaked me out, because I wasn't pushing too hard AND I was not wearing any heavy footwear - just socks. Watch out for that little pressure point.