Actually I never played the Wii version, so maybe I'm wrong. I know for sure the Wii version definitely has its issues too though, missing hit flashes, buggy audio like the mission complete track sometimes not playing, those are more trivial issues than input lag though. Also, no Gamecube d-pad support means crappy arcade stick compatibility (not a fan of wireless).
The PS2 version I've played and there's definitely input lag, it's especially bad in the first Slug which is my favorite, and why I sold it, really pissed me off. They delayed the hell out of the PS2 release so I'd be a little surprised if the Wii version was somehow unaffected, but I guess it's possible.
SNK Playmore is just a massive F up of a company. I can't remember specifically which game it was, I could probably find out on the neo-geo forums, but on one of their console releases somebody extracted the files and found SNKP had downloaded ROM dumps from the internet and used them in their official release with upload credits and everything still in tact on the disc. They're probably the laziest, cash-grab publisher in existence.
I'm still waiting for a flawless 1, 2, X, and 3 compilation on a single platform, preferably with the extra modes available on the Neo CD/PS1 releases. But it's only been, 12 years?