More me there are 3 main flaws

1) Animation
It's a case of having too many frames, the jumping animation for instance it takes forever to get to the key frame so it looks and feels bad. This is a case of devs going ape shit because of lifted limitations without wondering how negatively it impacts the game.

2) Enemy design/placement
There are several scenarios where the game dumps literally dozens of shitty low tier enemy at once. It's not fun, it's just messy. Like the whale that drops Metools or the birds in Search Man's stage. Again, another case of "let's do it because we can!" (as opposed to sprite limitations on NES/SNES)

3) HP/Energy gets replenished at each checkpoint
That's ridiculous, it means there are no stakes. You can take tons of hits, spam weapons, doesn't matter, it gets replenished all the time. X4 has the same issue but to a lesser extent, I wish there was a romhack for both that got rid of this.
If they were worried about running out of weapon energy when it is required (like the 2nd SHMUP stage), there were other solutions, like handing out restores in key places that don't disappear if you die, or make sure enemies drop them.

I don't mind the surfing/SHMUP stages, I thought they were quite fun

Still a good game, it's just weaker than everything else in the main series.