What if "mastery" skills worked different for bards than other guilds? Rather than relying solely on the mastery, it would be a combination of bardic lore + mastery or use bardic lore if higher. It wouldn't affect experience gain, just a flat out "you know a lot because you're a bard so you can do things that are second nature" kind of thing. This also ties into the jack of all trades angle.

Systemically, here's a few thoughts on how you could implement this.

Option A: Likely the cleanest option. Tie it into magic 3.0 and create a new spell. You would cast the spell and get +skill with a max of [ bardic lore - target skill] or [1750 - primary skill] (whichever is less) at 100% potency. Yes, you could conceivably nerf yourself if you overtrained a skill and undertrained bardic lore. Bad bard. Cast options: Melee, Missile, Offhand, Magic

Option B: Variant of Option A, but rather than creating a new spell, just roll these four groups into the four elemental transformations. Each transformation buffed that skill and bardic lore gave it a boost to that buff.

Option C: Passive average. Probably a little harder. Just do a CTR + F on all mastery checks and replace it with (example) [Primary Magic + Bardic Lore ]/ 2.

Option D: Variant of Option C, likely more powerful. Replace checks for mastery skills like primary magic with Bardic Lore if Bardic Lore > Primary magic.