Anteater IS indeed very questionable. X7 passes him off as a person that can figure people out using his cyberspace knowledge, on first glance this is not really as mysterious as the characters of Isoc and Serges. Of course, it is still quite a questionable feat how he accurately predicted certain matters in relation to X and Zero.
If you're going to relate Anteater to Wily, he certainly fits the bill in quite a few aspects. That is, if he didn't get controlled by Sigma, and if he didn't actually give X compliments for getting through his stage... Though, he does very craftily verbally trash X, and it's not like X's success in the stage meant upstaging Zero..... Also odd, he still seeks data on Axl whilst he has been a Red Alert member for some time...
All in all, I think Anteater exists to muddle the waters a bit. Showing us weird old coots like that also can exist without naturally relating to Wily. Kinda like a way to avoid suspicion of Isoc and Serges.
Also, most of Anteater's words reference to the ZERO-series, not so much to Wily...