Whoa-ho, what a bump!
I've been playing this a bit in Ootake, and liked it enough to order a copy. I played quite a bit of both the PCE port and the MD Special revision, enough to share some thoughts.
I think people tend to like
Funari's* MD version based on that it looks better and is far easier. In fact, it's extremely easy - enemies rarely get the chance to fire a shot at you, and once you are powered up, you can expect to cruise through half the game before enemies muster up the courage to block your advance. It's pleasant and showcases some groovy graphics, but it doesn't win over any fans through its ho-hum appeal.
Kaneko/InterState's PCE version, by contrast, looks like a second-rate NES game - though with the exception that it throws a lot of stuff on the screen without flicker or slowdown. I didn't even know the second stage was supposed to be underwater until I played the MD version. What it lacks in looks it makes up for in playability. The game is far more aggressive (the opening bit is hilariously designed to f*ck over players non-stop), and it rarely lets up in that aggression. The smaller sprites make for tighter maneuvering, and the end result is a pretty enjoyable game. The game has a lot of R-Type segments where if you memorize where to position your ship during some crucial moments (like the... crate-snake things) you will have a far better time of it. There's usually never a power-up too far away after death, allowing for some semblance of recovery.
I wouldn't call the game my favorite shooter on the system, but it offers up some pretty furious fun. I encourage others to try it out via emulation (or the MD port, if things are too difficult!).
*I can't help but link to this site. It's so addicting to finally get a sense of which companies were actually working on these ports as opposed to the generic publisher labels like Taito and NCS/Masaya (the latter of which barely seems to have done any games themselves on the PCE).