Most PCE shooters in my experience are pretty easy. After a week's worth of practice you're usually good enough to 1CC a shooter without thinking too much of it.
Paranoia/Psychosis is a snooze until the final level, which is actually a little bit challenging. The second loop is nuts though, but that's for the hard-core. Heavy Unit has a hard beginning and an easy everything-else-for-the-rest-of-two-loops, even Kyuukyoku Tiger is pretty boring until the second half of the game.
Legion is a hard game because it's a lousy game. Poorly-designed and oozing with Telenet """quality"""
To its credit, it's one of the hardest PCE shooters, but not for reasons that are worthwhile.
Rayxanber II is a game that is exceedingly strict on memorization and execution, and it is also one of the hardest games on the system. It's an acquired taste, since it goes far beyond IREM in terms of memorization so it can seem excessive in terms of "be in this exact spot at this exact time." Since it has no power-up levels to speak of, recovery is fairly painless though.
The Konami games at higher loops are pretty worthy of the label of "hardest." On the plus side, games like Gradius II, Salamander, etc. are actually fantastic games, programmed by competent devs so their difficulty is a welcome challenge as opposed to eye-rolling, head-shaking frustration offered by lesser studios (see: Telenet).
I recently beat Compile's Xevious remake (Fardraut) and it's a fairly tough game, because it seems to relish in belching bullets all over the screen - a little sloppy at points honestly, because it seems like you NEED a shield to get through some parts. Since I could 1CC it though, it can't be that hard.