While I agree with parts of your assessment, it doesn't apply here very well:
Sneak attack on a Paladin... yeah, no.
Crit-fishing... OK with critical feats (which come obscenely late in levels), but relying on flaming burst means you have to shell out for two costly weapons instead of one if you use TWF. In this case, TWF is strictly an inferior option (not to mention that flaming burst and its ilk are weak enchantments in the first place).
Weapon-specific feats... which ones were you thinking of? I can't think of any good ones off the top of my head.
But the reason I chose to reply is the "...using, say, holy from his weapon bond...". That's exactly what the OP was asking about: can you apply your weapon bond ability to two weapons as easily as one? Your implication (you can) is in line with what other posters here argued, and they argued that way to make TWF a less terrible option.
I'm really pointing out that you've got to consider how the abilities combine to get an idea of whether changes are unbalancing.
I'm not actually sure whether it's enough of a power up to be unbalancing but it needs a bit more analysis than "sure 2-weapon fighting is underpowered"
Generally 2-weapon fighting doesn't compare overly well with a 2 handed weapon but it can be pretty powerful if there are options to boost the damage.
Sneak Attack was an example of something that makes 2 weapon fighting powerful.
Flaming Burst can be added by the Weapon Bond (as can Holy or axiomatic), if it affects both weapons then you could get +4d6 damage against, say, a demon on every attack -admittedly not until 14th level. If it's the target for a smite at that stage it gets +4d6 + 14 damage on each hit -> plus anything else you normally have
If the weapon bond applies to both weapons you do away with some of the requirement to keep both weapons up to date, how many adventuring days do you really have more than 5 minutes a day of combat at 5th level or, say, 10 minutes a day at 10th?
as far as single weapon feats go Improved Critical isn't bad (especially with Kukri's for a 2 weapon combatant, 15-20 threat range, and smite damage is multiplied on a crit) I'm not sure if there's anyway for a Paladin to get them without multi-classing into fighter but the Weapon Specialization, greater weapon focus, greater weapon specialization combinations have a fair impact.