There's been a lot of speculation on this subject, but from experience, I can say that you need to pick your poison. If you go for a ton of shield caps, you'll be very vulnerable to close-range alpha and DPS attacks. If you choose to overload on rechargers, you'll be incredibly vulnerable to lock-on swarms(5-20 sets of beam missiles arrayed for maximum penetration on impact). If you really don't like either of these choices, you can go for 1:1, which gives you 10% passive non-combat recharge (.006% in combat). It's a good balance that leaves you with both problems, but to a lesser degree.
Many folks on the MFleet server like to swear by their oversized shield capacities. Once they go down, though, you're pretty much dead in a world of the AI turret gods. Personally, I find it hilarious to carry less shields, but have them almost instantly pop back to 100% after losing them all to a missile. You'll take surface damage, sure, but you won't be cored if you built your ship well (and the enemy didnt bring AP sniper AI turrets). It also makes you incredibly annoying to finally kill.
This is actually the principle I use on the Executor's combat version - Sure, I could carry 50mil shields on it, but i'd only have 500k recharge. By dropping it down to around half that, I can carry almost 3mil recharge - which amounts to around 90k a second in combat. Small ships literally cannot damage the vessel due to this recharge, and because the ship is so damn huge, it's more than likely that you'll have to drop the shields two-three times before finally coring it.
That's titan class though. Cruiser and below is a tough choice - you really need to chose a role for your vessel.