Then again, people managed to get into a lot of numbered games lately without bothering with the predecessors. Witcher 3, MGS V (I know it's not "5", but come one, most people thought it was), Final Fantasy, Saint's Row 3, etc.
Alright, how many of those IPs have a rocky and less than stellar record when it comes to their numbered sequels? The only Witcher game not on consoles is the first one, Metal Gear's low point was "too many cutscenes", Final Fantasy's localized releases got the numbering right because Sony wanted to stick it to Nintendo.
And uh, Saints Row is a franchise zombie, I don't know why you listed that.
Point being, people have good memories of those IPs beyond the first one they played.
Valkyria Chronicles, on the other hand, people really only liked the first one. The second one was Objectively Bad, and the majority can't form an opinion on the third one because Sega refuses to localize it. So that's a 33% rate of games in the series that are liked by the majority, with the missing 66% counting for VC games that had a number in their name.
Compare, say, 100% for The Witcher, 80% for Metal Gear, 85~% for Final Fantasy.
This isn't a matter of people being intimidated by a high number and thinking they need to try out 1, 2, and 3. This is a matter of 2 and 3 being tainted numbers that Sega or the fans won't be wanting any reminders of hanging around.
EDIT:
For further proof, the VC forum on Sega's website purged all the VC2 related stickies when the PC release of VC1 came out, leaving only the old VC1 stickies and the new ones about the PC release. Along with reverting to the original VC1 background image for the forum. As far as I'm concerned, Sega is shoving VC2 down the memory hole.