[Saulot]

I use a combination of tactics to go around this problem. None of them are optimal or perfect.

For some units, I simply use a weapon that seems similar to it, firebreath being a common example.
For other units, I simply use an already made weapon as a secondary effect as you do. A good trick to make sure secondary effects take effect, is to make the primary weapon have the following qualities:
1 damage
armornegating
dt_cap
100 precision
secondaryeffect XXX

What this in effect does, is throw the effect you want at whatever square you want, 100% of the time. It has the minor unfortunate side effect of forcing 1 armornegating damage on the target in addition to whatever you wanted to do (set them on fire, paralyze them, whatever...).

So far though, for a more realistic fireball weapon, I would wait till august when the next patch is expected. The AOE and secondaryeffectalways commands should be fixed then.

As for flysprites, I can't help you with that, I've had no luck getting anything above what was suggested in the modding manual.

Edit:
Oh, and aoe effects do work as secondary effects, one of my traps is the aoe effect leg chop, which affects the whole square.

Edit2:
I'm pretty certain copying wand of wildfire would do nothing, just give you the base weapon (some sort of scepter which hits ethereal units)