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The only ones I can think of are the first three, since they all connected together rather nicely. Not that they have much story to begin with, but when you see it from Super's perspective nearly everything fits.
I like turtles.
The Prime series doesn't have that many plotholes.  Other M was the only title to introduce glaring problems with the continuity and series mechanics.
The only problem with the continuity that I can think of is Samus's personality and how she reacts to the Ridley scene.

Sure, you could argue that evolved Metroids were already immune to Ice, but in Metroid Prime, there are unevolved Metroids that are affected by any weapon and nobody complained then. Stuff like that IS able to change. And yes, it was explained in MP3 sorta (note sorta), but couldn't the Metroids in Other M be explained in a later game too.

And how does one exactly retcon a series mechanic?
ohh jeesus.. -_-
If I had to wager a guess, Super Missiles and perhaps Power Bombs.
What? I don't get it. Super Missiles actually work exactly like they did in Prime. Power Bombs... well, they have a similar blast radius as the 2D PB's. The Prime series' Power Bombs had a small blast radius.
Edit history:
Turtle: 2010-11-22 04:08:06 pm
I like turtles.
I actually kinda liked Super Missiles as a separate item better.  Although I never got the point of having limited ammo for Power Bombs in the 2D games, considering they're used to destroy their corresponding blocks more often than as a weapon.

They either should have very limited ammo and crazy attack power, like in Prime, or they should just forgo having ammo.  Especially if the only purpose of Power Bomb expansions is to pad the game (Fusion, Zero Mission).
Edit history:
UchihaSasuke: 2010-11-22 11:07:34 pm
my umbrella goes directly to Bankai
regular missile expansions are more guilty of padding the game since they're practically useless almost every time in almost every game.

though Fusion's PBs were like a slap on the face. the initial amount is more than mp1's maximum and on par with mp2's max. SM is the only one i felt item amounts were distributed more reasonably and it still had a bit excessive missiles.
Edit history:
Prime Hunter: 2010-11-23 12:05:47 am
The only real times where having more missiles is key to your survival are in Metroid and ROS. You needed them for the Metroids in ROS, but in the original game if you don't have enough missiles every enemy become much more deadly to you because of how many beam shots are required before they die. Otherwise, yeah, once you get to a certain point getting more missile expansions is pretty much useless unless you're going for 100%.
I like turtles.
Missiles are more useful offensively than Power Bombs, though, because they have a decent rate of fire and damage output relative to their rate of fire (this is inverted in the Prime series, especially Corruption).  I actually used missiles a lot in Super and Zero Mission...

Of course, I needed a lot more of them than I do now because my accuracy sucked back then.

The only game in which missiles aren't a viable attack option, though, is Corruption.  Horrible, horrible, useless sissy-missiles.
The only viable attack option in that game is hyper mode.
The next Metroid game should have regular bomb expansion packs.
One shall stand, one shall ball.
bomb parts, collect four for another bomb!
Um... no. Just... no.
I like turtles.
Am I a horrible person for thinking that an upgrade which would allow you to lay more bombs simultaneously wouldn't be such a bad idea?
It would just be somewhat useless.
Remote Bombs
I'm sure they could find a way to use Bomb expansions/upgrades. Maybe not a good way, but a way that works. Heck, seeker missiles don't seem all that great at first, but they work fine.
I like turtles.
Seekers are moderately useless in Echoes and Corruption, and completely useless in Other M.
At least they are used in battle sometimes in Echoes and Other M. I can't think of a moment off the top of my head where you'd use them to attack in Corruption. But yeah, I'll agree with you that seekers were more or less thrown in to all three of the games to block our progress and act as puzzle solvers.
my umbrella goes directly to Bankai
man, poor Helios dies so easily that he can't stick on our minds...
Heh, oh yeah, I remember that now. I usually just blast him with Hypermode and Screw Attack so that I only need seekers if I'm not doing that well against him.
Quote from Turtle:
Seekers are moderately useless in Echoes and Corruption, and completely useless in Other M.

What ISN'T completely useless in Other M?
my umbrella goes directly to Bankai

it is as useful as the dashes in mp1.
I like turtles.
Charge Beam.
Screw Attack.  Actually, it was nice to see Screw Attack as a feasible offensive option after its decay in Echoes and Corruption.*

*Not counting the Emperor Ing and Gandrayda tricks, which weren't intentional.