I think one of the biggest culprit for the stagnation of the genre is the bomb. I'm not sure which game came up with this, but it's probably Raiden, or at least that's the one I remember seeing in the arcade. Raiden is a standard suppression type shooter where if you died once you're probably doomed, so they throw you in some bombs so you can at least make some attempt at a comeback and it works well enough, though even there you start seeing problems as on the harder stages you basically just drop your 3 bombs and then immediately die and get 3 more bombs and that's a far more effective way of beating the stage than actually trying to avoid the stuff.
But in the newer games you basically have bombs as a 'rich gets richer' deal. This is even true in Ikaruga where you'll see the top video plays makes heavy use of the charged shot (equivalent of the bomb) since it does massive damage and there's really no reason to not use it, though at least it didn't make you invulnerable. This means if you're good enough the game actually becomes easier. On the other hand for someone struggling to figure out how to soak up enough bullets to charge up the shot you might never fill your meter before you die, and then you decide to look to see how the expert do it and it's not unusual to see a replay where a guy has the charged shot fully charged at all times. There are way too many bullet hell games where you can see top level playing all revolve around abusing bombs, and makes you wonder why you're trying to get good at this shooter and learning the patterns when you see the top players just keep on chug bombs in the general direction on the enemy. I assume there are two primary motivation for playing a shmup:
1. Blow a lot of stuff up.
2. Dodge stuff with mad skills.
For #1 you don't need the bomb because your generic power up system has more than enough for that. For #2 you obviously aren't dodging anything when you get a screen clearing bomb. It's funny that people into these genre seems to frown on god mode and yet you'll see a replay of a top player just drop a bomb on the boss, hug it and use the invulerability frame to kill the boss before the invulnerability frame ran out, which takes no skill at all beyond knowing how much health the boss has so whether your invulnerability frame lasts long enough to take out the boss or not. Honestly I think people just aren't as good as they think they are. Just like in Civ 5 everyone says they cleared it on Deity but the achievement shows only 1% did it, I'm hard pressed to find most people can even clear the 'normal' setting of a modern bullet hell game even with your standard 3 continues let alone without. But you can do it if you abuse the bomb and since the average bomb in the average bullet hell games does at least 20% of the final boss's health bar and you start with 3 of them, this means the game gets stupidly hard assuming you'll just bomb nonstop and I really don't think that's how a serious shmup player would play the game. It's probably not a coincidence that all the Touhou challenge levels, especially the fan made ones, has boss that start with complete bomb immunity because otherwise anybody could complete them on one credit.
They really need to back to stuff where you could get powerups like Gradius/RType as long as the game has a reasonable mechanism to ensure you shouldn't immediately restart your game if you die even once. Sure, the bomb is one way to solve this, but it's just not a good way to solve it, especially when you've the standard '3 bombs per life' game where you'll commonly see people simply die to get more bombs because it saves time and usually gets you more score anyway for killing the boss faster. UN Squadron had one Mega Crush you can use (2 if you bought the super plane) and that seems about right for the number of emergency bailouts. You didn't use the Mega Crush unless you're about to die or you just need to do a ton of damage immediately and that's how bombs should be used, not something where you just drop 3 of them as soon as the boss becomes vulnerable.