A few little things.
Firstly, Spell Resistance. With the Arcane Archer's slower spell progression (barring the proposed fix), a Wizard 12/Arcane Archer 8 is looking at a caster level of 16. Not bad, but a little low for a 20th level character, when it'll be facing down nasties with SRs near 30 or above. To counterbalance this, I would suggest that the AA be able to apply their Enhance Arrow bonus (or half, rounded down) to all rolls made to overcome spell resistance. That should make up for their impeded CL.
Secondly, how does Split Arrow interact with Manyshot? I can see an AA unleashed a volley of 6 arrows, each imbued with a disintegrate spell. Pretty high damage.
Last of all, a minor critique and/or wording complaint. You don't specify in the prerequisites that you must be able to cast Arcane spells of at least first level. I know the name kind of implies it, but I'm a stickler.