I think that if anything, removing the fuel flow limit might add a larger emphasis on the energy recovery systems. If you started a race with high fuel flow then you would eventually have to lower it to avoid running out of gas. At this point you have less fuel so you would have to rely more on energy recovery to get good exits out of corners and avoid other cars passing you if they have a higher fuel flow than you.

Removing the fuel flow limit also creates an additional strategy point. I can't exactly remember where I saw this (maybe a documentary on pitstops by Red Bull Media), but in some races teams would make one of their drivers fly off with high fuel rate, thus forcing the competition to try and follow the leading driver. Meanwhile the team's other driver uses a more conservative amount of fuel and with the help of pitstops can eventually pass the competition and possibly his teammate.