Classic and EXE are far more likely than X.
Not so much EXE, because he was also de-confirmed. Remember, Americans (who MvC3 is directly marketed towards) largely don't share the EXE love that Japan does.
X's popularity was mostly killed with the lovely string of titles called X5-X8 (put your personal feelings for the titles aside, you know they all have issues.) MHX tried to rebolster it, but it just didn't give the series that vital resuscitative spark it desperately needed.
It was also due to poor placement/timing. Any body could have told Inafking that releasing the Rockman game duo on the PSP, during the time frame they were released, was a BAD idea. The PSP wasn't a hot gaming commodity in Japan until
Monster Hunter Portable made it so, and gave the PSP a "Pokemon" type of phenomenon of its own.
I'd be willing to bet that if Inafking and Capcom had waited a little while longer, and released the Rockman games AFTER the MHF boom, they would have been much better received, just like a whole slew of other PSP games/series were made much relevant thanks to MHF. To me, it's pretty telling when both
IHX and RockRock alike a had a brief surge of sales posthumously , because a whole new slew of PSP owners finally got around to trying those games out and actually saw that they were a decent time to be had.
And another note, X was at the top of poll data taken from Nico about what Capcom characters would Japanese gamers like to see in the game. Results as follows:
1. X (Megaman X)
2. Date Masamune (Sengoku Basara)
3. Vergil (Devil May Cry)
4. Megaman.EXE (MegaMan Battle Network)
5. Leon Kennedy (Resident Evil 4)
6. Pheonix Wright (Ace Attorney)
7. Ken Masters (Street Fighter)
8. Cammy (Street Fighter 2)
9. Tabasa (aka Tessa, Warzard aka Red Earth)
10. Guy (Final Fight)
11. Cody (Final Fight)
12. Sanada Yukimura (Sengoku Basara)
13. Kasuga (Sengoku Basara)
14. Bass.EXE (MegaMan Battle Network)
15. Maeda Keiji (Sengoku Basara)
16. Gene (God Hand)
17. Batsu (Project Justice)
18. Akira (Project Justice)
19. Jedah (Vampire Savior)
20. Jin Saotome (Cyberbots Full Metal Madness)
21. Saki (Quiz Nanairo Dreams, TvC)
22. Kaijin no Soki (Onimusha Dawn of Dreams)
23. Leviathan (Megaman Zero)
24. Kirin (Monster Hunter, A Unicorn Monster)
25. Grey (Megaman ZX Advent)
26. Roll (Megaman)
27. Rock Volnutt (Megaman Legends)
28. Harp Note (Megaman Star Force)
29. Alex (Street Fighter 3)
30. Ingrid (Capcom Fighting Jam/Evolution)
31. Captain Commando (Captain Commando)
32. Chuck Green (Dead Rising 2)
33. Edward (Falcon? Fokker? Power Stone)
34. Oda Nobunaga (Sengoku Basara)
35. Ryu (Breath of Fire)
36. Demitri (Darkstalkers)
37. Gallon (aka Jon Talbain, Darkstalkers)
38. Red Arremer (Ghouls n' Ghosts)
39. Zack (Treasure Island Z: Barbaros' Treasure)
40. Sonson (Sonson, MvC2)
41. Regina (Dino Crisis)
42. Sheva Alomar (Resident Evil 5)
43. Nash (aka Charlie, Street Fighter Alpha)
44. Vanessa (P.N.0.3.)
45. PTX-40 (Lost Planet)
46. Leo (Warzard/Red Earth)
47. Dhalsim (Street Fighter 2)
48. Unknown Soldier 1P (Lost World)
49. Sigma (Megaman X)
50. Yagyu Jubei (Onimusha)
51. William Gray (Dark Void)
52. Hayato Kanzaki (Star Gladiator)
53. Maximo (Maximo)
54. Michelle Heart (Ares no Tsubasa/Legendary Wings)
55. Lou (Three Wonders)
So it would seem safe to believe that, no matter how poorly Capcom may have treated X in these last few years, he's still loved in Japan just as much as he is elsewhere. It's only a matter of time before Capcom will actually capitalize on that...