According to Spong Metroid Prime Hunters will be an online compatible game, with the internet mode being "along the lines of Halo 2".

Spong are reporting that Nintendo have told retailers in America that Metroid Prime Hunters for the Nintendo DS will have an online mode. While the source, a US retailer, is a bit less trustworthy than Nintendo themselves it is still interesting to consider the possibility.

“The game will be fully online and we were as surprised as anyone. Nintendo told us that we should 'think along the lines of Halo 2, deathmatches, online leagues and so on'. It is going to be shown running online at E3 and will hit [in the US] in mid-summer.” said Spong's source.

As stated this may not turn out to be true, but I guess we'll have to wait until E3 to find out.