Formula E is in it's infancy, and right now is still drawing in fans and support.. Now is the time for stunts like this...
It won't be around forever, but for now it provides an additional measure of interaction and excitement in a sport that is already hard to get into if you're not willing to follow the non-race drama (the "circus" as they put it).
The same thing could be done for normal F1 cars - for example, by raising the RPM limit, power output or drag reduction for a few seconds. In fact, with KERS, F1 drivers already have the same kind of boost but without the voting.
FanBoost is a gimmick, and even F-E management acknowledges that it has virtually zero impact on the race itself.
It's a 5-second ~5% power boost.. That's not going to change anything, and neither would letting the cars run at 5% more power in general without it..
I am sure that teams are innovating battery and motor just fine even with this minor limitation..
Don't you think if FanBoost was actually crippling or limiting innovation in the way you're assuming, the teams would cry foul? That kind of counter-productive decision would go against one of the main reasons they do these racing leagues (to innovate!).
As an aside, all motor racing is "crippled", as you put it, by rules and regulations designed to provide a reasonably level playing field.
Even Formula 1 has all kinds of limiting rules and guidelines that prevent teams from simply building the fastest/lightest/most powerful cars they can possibly design, and that's intentional.
Unlimited racing basically becomes a bloodbath and a contest of who has the most money (which is a problem that F1 still has). Yes, fan boost is a gimmick, but don't get too upset about the purity of 'artificially crippled' racing.
It's really not the problem you're making it out to be.
FanBoost gives one driver a one-time 5-second ~5% boost to use during the race..
That's not going to change race outcomes in any significant way, and even Formula E acknowledges that it has (intentionally) virtually no impact on the race..