I would've liked to see more out of Yumekobo, since I loved Blazing Star. (Pulstar was crap though...)
Seibu (Or Moss) needs to make a Raiden Fighters sequel, or maybe Viper Phase 1. I'd be especially interested to see a Raiden Fighters game that constituted both the 1 and 2-styled levels and a 'simulation mission' like Jet. Perhaps they could loop into one another on insanely hard difficulty provided you do well (Like Raiden DX). Presumably the aircraft would all be jet-age aircraft, then, or perhaps turboprop power. Or just keep it piston engines, like the Sky Crawlers or something.
I've always wanted to see a sequel to Gunforce 2 and Dolphin Blue. The original teams aren't there anymore, now working on Metal Slug, but given that Irem did so well without them (R-Type was indeed made by the team who would later make Metal Slug) I've got hope. Likewise I would pay to see Noise Factory make either a Metal Slug-like IP (Kind of like MS4 but entirely their creation so Metal Slug fans wouldn't rage) or somehow obtain the license to make Undercover Cops 2.
This isn't really that shmuppy but The Outfoxies needs a sequel, or some kind of similar game. It's weird how the only game as of late that even comes close to its formula is Super Smash Bros., and even then that's more about NINTENDO CHARACTERS UNITE! than it is about "killing your opponent by any means". Oh and a Monster Maulers-esque game. With tentacle rape.

Wouldn't it be funny if Toaplan decided to reform again instead of split into four different companies? Then we'd have games that unite all of Cave, Raizing, Takumi, and Gazelle's ideas!
If there was a sort of gallery-shmup revival (Like Space Bomber) I would probably play it.
I liked R-Type Leo so maybe a sequel to that?
A new Giga Wing would be nice.
If the Metal Slug devs made a new R-Type under the name of Last Resort 2 or something, then that would be rather cool. After all, they're the ones who started it all.
Does anyone else want Death Label games for the DS?
R-Gear sounds like a good idea, but unfortunately Earth kind of went asplodey in the end of Rayforce so I don't know how that would fare.
If Raizing made a shmup...ANY shmup...sometime recently, I would play it.
Ace Combat DS? Like Advance but...even better. Shame they'd probably just give it shitty 3D graphics instead.
More Elevator Action.
Shock Troopers 3. We miss you Saurus ;_;
An Armored Warriors sequel? (Okay, admittedly that was not shmuppy)
A Vs. Shmup that doesn't involve lolis. Change Air Blade was okay, but I was thinking of something slightly more...fair or so...
1945: The Final Battle sounds like something I want.
A View Point that isn't complete crap.
Sorry for not following the 'A sequel' part but there's a lot I want to see ;_;
Edit:
What about Twin Eagle 2Ed Oscuro wrote:Thundercade
instead Seta went on to make shit with amazing 30 second digitized music loops, YEZ They forgot the fact that Thundercade was cool because you could blow up nearly every building onscreen in glorious animated crumbly detail, not just trees and houses that go "poof" as well as being able to shoot watchtowers out from under soldiers without their minding. Of course, scoring and game design seems to have been pretty much random when it comes to Seta shooters.