It doesn't sound like a bad idea; it also means that you end up with more holes in your shield wall the more boosters that you stack. But I kind of a agree with that the biggest attraction with shields is their absolute protection that is provided for all modules.
A hybrid idea is to perhaps treat shield boosters as individual shields themselves, and assign a "layer" to them.
Consider a ship with 2 boosters:
Base shield: 500MJ (broken regeneration rate: 4.0MJ/s)
Shield booster A: 50%
Shield booster B: 25%
Total shield: 875MJ ( 500*(1+.5+.25) )
Then assign a layer to them:
Shield booster A: 50% (Layer 1 - 250MJ)
Shield booster B: 25% (Layer 2 - 125MJ)
Base shield: (final layer regardless of layer settings - 500MJ)
During combat, layer 1 is the outermost shield layer that take damage first. Once the first 250MJ of shielding is exhausted it goes into broken recovery mode (Using the base shield broken regen rate), and so will not come online until it recovers 50% of it's capacity (this also means use lose any resistance bonuses conferred from that booster until it comes online again). During this time a small hole opens up in the vicinity of the booster that can allow weapons to damage the hull or modules.
Any damage that still hits the shield will take then from shield booster B's capacity until Shield booster A has recovered (by recharging to 50%, the same way the current system works).
Heh, just thinking about it however, makes me wonder if this would actually be more beneficial to the defender rather than the attacker. With multiple small shield boosters all placed into recovery mode, you may have many holes in your defence, but your regeneration rate is effectively additive. ie in the case above if both boosters go down you have two holes in your shielding, but your effective regeneration rate is 2*4MJ/sec or 8MJ/sec even if you don't see the results of those MJ's until your shield boosters come back online.
In the case that your base shield then gets taken out, while your shield boosters are regenerating, I think perhaps pausing all currently regenerating boosters until your main shield comes back online might be a fair compromise (eg, shield boosters work like shields as long as your base shields are still up; they aren't completely stand-alone shields in their own right).
Small fast ships with tiny bi-weave shields, and several resistance based shield boosters would probably become rather a nuisance to defeat, since by the time you've managed to peel away 2 or 3 booster layers, all of a sudden the first layer comes back online, and those small open holes in the shields will be harder to hit and close rather quickly.
hmmm....I don't know maybe this idea might make things worse
TL;DR:
-Treat shield boosters like full shields themselves that inherit the regeneration rates of the base shield.
-When the damage to the shield exceeds the capacity of the booster, have it go into broken regeneration mode and then open a hole up in your defences in the vicinity of the recharging shield booster.
-If your shield gets taken out while all your boosters are regenerating, pause the regeneration of those boosters until your shield comes back online.