I think C2 is the best 2d game dev tool out there. To go 3d, Scirra would be playing a pointless game of catch-up against mature 3d tools with large dev teams.
The biggest challenge for most indies is simply finishing a project. It is hard to keep an unpaid team together for an epic project. And if you finish, 3d does not increase your chance of success. It will still most likely be a flop.