I've been looking, but the only thing banks support enough to actually allow the movement of funds seems to be quicken. Are there any alternatives that allow similar levels of control?
Depending on your platform and country, there are alternatives to Quicken.
Most banks will say "we only support Quicken" to lessen their technical support burden, but under the covers they mostly use a standard protocol, OFX. That means any software package which supports OFX should work. On the Mac platform, iBank is one example.