A couple of titles that come to mind for me are
Sonic R for the Saturn, and
Space Channel 5 on the Dreamcast.
The first time I played
Sonic R, I think I was expecting something more along the lines of Mario Kart. The controls felt loose, characters seemed to slide all over the place, and music seemed really out of place. After putting more time into it, I got the hang of the controls, and got pretty good at it. I was getting all the Chaos Emeralds without any problem at all. The music ended up being one of my favourite things about the game. Songs like "Can You Feel the Sunshine", and "Super Sonic Racing" are still stuck in my head. The fact that it seemed so out of place in the game, just made it even more enjoyable
.
Daytona USA is another one of those games where the soundtrack played a huge part in increasing my enjoyment of a game that I didn't care all that much for at first.
I got
Space Channel 5 for around 99 cents (factory sealed) around the time that Dreamcast games were dirt cheap everywhere. I really liked the atmosphere, but I just couldn't make a dent in the gameplay. Ulala's animations for the moves kept throwing me off, and I just couldn't keep the rhythm. A while after that, I found a sealed Japanese Dreamcast copy of
Space Channel 5: Part 2 on eBay for around $40. I wasn't even aware there was a sequel, but I figured that it was worth a shot.
Once I got it, I was blown away by just how much they'd improved on the game. The animations would speed up if the button presses dictated, so it was much easier to get the hang of everything. It ended up being one of my favourite games of all time. After beating it, I decided to give the first game another shot, and ended up loving it. I managed to beat it without much issue, and consider it one of my favourite Dreamcast games out there.
Skies of Arcadia took me a bit of time to get into too. I played it not too long after finishing
Grandia II, so the battle system didn't really do that much for me. I didn't really get the hang of what colours trumped what when switching weapons around. The amount of random battles didn't really bother me that much, but seemed like a bit of a step back from everything else I'd been playing at the time. Over time, it all really grew on me though. The personality of the characters, and the sense of adventure drew me in, and again, it's one of my favourite games on the system.