I may be wrong, but:

- SQ-A has MLU (it's old SQ that hasn't)
- when battery runs out you may still shoot SQ-A at 1/500s, but you can't fire SQ-Ai (not a real problem, batteries are cheap)

SQ-Ai body has a couple of improvements over SQ-A:

- 'Bulk' time;
- TTL flash metering

SQ-Ai accessories, which you can use also with SQ-A body, were also improved:

- ISO dial on a film holder was moved to a better position, you can set correction with a prism view finder mounted; ISO setting was extended to 6400
- new AE-i view finder is much more sophisticated, allow exposition compensation, spot metering, exposition hold - perhaps the best thing of SQ-Ai line, that's usually reflected in its price
- detachable motorised winder (doesn't fit to SQ-A); in case of SQ-A you can only choose motorised body

Don't buy any Bronica without WLF, unless you have one - this simple thing sells more expensive than the body itself.