What happens to bonus weapon slots in 2.x patches?

Just starting another run through the game, and still on v1.3 as that remains the current version in the Mac App Store. I am planning on taking Coran this time for his crazy dex and bonus 3* bow skill, but understand that there is a new way of assigning character levels once I get the 2.x series of patches. Does that mean we lose these quirky character bonuses for Coran, and Haer D'Alis in BG2? (And possibly others I am forgetting). Is there some in-game way to restore that skill through the new level-up scheme? Or do I simply not understand how the new scheme works?
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Coran will always have his bonus proficiency.