Honestly, SNK can't win for losing.
The Metal Slug series is basically the ne plus ultra of 2D shooters. There are none better. You might be able to make an argument for some other series, probably something by Cave or Treasure, if you limit the field to 2D side-scrolling shooters in which you are not in an aircraft, but that's sophistry at its finest.
Metal Slug is pretty hard, yeah, but it's relentlessly entertaining. It's extraordinarily well-animated on levels that nobody else has ever even really tried to reach. SNK put some serious work into this series, and it pays off.
Of course, the flip side here is that they don't seem to be able to port it to other systems to save their lives. Metal Slug Anthology came out on the Wii two years ago, and got raked over the coals for having weirdly gimmicky controls and loading screens every time you turn around.
Metal Slug 2 on the Virtual Console is easier to deal with. It's quite playable with the normal Wiimote, although grenades are fixed to the A button, so you have to choose between moving or throwing bombs. (That said, when did you ever have to throw grenades on the run?) If you've got a Classic Controller around, it works a bit better.
The Virtual Console MS2 is a straight-up arcade emulation, to the point where you can't pause it; it's as though you went up to an arcade cabinet and put five quarters in. There are no load times to speak of, and the game is absolutely amazing; the second stage is one of the best in the series.
Unfortunately, there's a bit of a trade-off here. For whatever reason, there's a fair bit of slowdown onscreen whenever there's a lot going on, and this is Metal Slug, so there's always a lot going on. It's not game-breaking at all, but it is there when it wasn't there in Anthology.
If you didn't pick up Anthology due to the bad reviews, MS2 on the Virtual Console is probably a better purchase. A bit of slowdown is a small price to pay for one of the best shooters out there, especially when you can actually play it.