Very hard to say if the skills carry across but for me each shoot em up either goes to the next level of ridiculous or down the R-Type/Nanostray route, then you have your bullet hell games, then your boss rush games, your old school 2D scrolling shooters.
Across genre's you can map your skills and the bullet hell games which I tend to play its all about working out the patterns and then doing the smallest twitches of a controller to get between the bullets coming at you. Your side scrolling ones is literally learning the patterns of what's going to come on screen and in what wave and the old 2D vertical shooters its simply hit what you can as it comes on screen.
It's a dying, well maybe I should say limited section of the gaming world now that people won't buy them in the majority though there are really huge groups all over the net who love, eat and sleep shoot em up's. The problem is, my generation, 80's kids and those through the 70's grew up with the spectrum, atari, c64's and amiga's that were littered with shmups by the bucket load. The early 8 bit and 16 bit consoles keep them coming and then the Playstations and Xbox's hit the market to cater for the newer generation of gamers and the shmup trickled off. I suppose when these games land on the market its the likes of myself buying them. Not sure why the shmup doesn't appeal to the younger gamers of today. Would be interesting to get the view of a gamer who's first contact with a shoot em up was the likes of nanostray on the DS, or the raiden series in the states.
It does seem though that the supply of shooters now is either through XBLA, PS Store or Wii Ware You have your geometry wars, 1942 and Ikaruga on XBLA, not sure whats on Sony's and Nintendo's online services and then the only other one I know that is coming to XBLA would be Raystorm but once again a rush of trailers for it and it was shown off at E3 last year and then nothing. No release date on the devs site and nothing showing on the XBLA release lists. Fingers crossed Raystorm HD will still be released. The last one I bought on XBLA was Death by Cube and it's a bit of a let down.