Hmm. The thing is, raised shields just means that fleeing opponents always get the advantage they already have, especially if they're firing off zero-Flux weapons behind them.
I get where you're going there- raised shields means some fighter protection- but in testing, in a universe where fighters aren't crippled, speed-wise, vs. Frigates... just having fighters be a bit faster than base Frigates is almost enough (granted, high-level Captains, SO and other things can tilt this rough balance once again).
I agree with the default flux boost being 5%, except that the issue was with Carriers, in particular, IIRC; in that case, why not simply forbid them from having the Flux boost... or cut their base speed enough that it doesn't help, or make the speed boost a per-ship percentile, and they simply don't get any?
Honestly, if we're talking about tweaking how the Flux-boost works in general, I think a per-ship percentile might be best; then we can have "interceptors" which get a clear advantage in chases vs. others that don't, and hand out bennies to balance the lot. The rule being that it's flat regardless of ship type, class, anything has always felt odd; it's a huge benefit to Capitals, in relation to their base speeds, but is less-meaningful for the fastest Frigates with Captains who also boost their top speed (except that here, it pushes them right out of Vanilla fighter speeds entirely, causing endless kiting issues in these long, drawn-out endgame scenarios).