Hi Andrew,
Her'es my 2 cents...
Separate Aileron/Flap
Pros:
- Better aerodynamics. Ailerons more effective at the tip, inboard flaps promote stability.
- Flaps more effective (drop them further - or build slotted flaps)
- Reduced adverse yaw. (just because you use a symmetrical airfoil don't think you'll get away without it)
- Looks better (IMO

)
Cons:
- More complex. Requires more servos, more planning, better execution.
Flaperons
Pros:
- Foolproof to install. You almost can't go wrong and it's really easy to produce a good quality installation.
- Sturdy.
- Simple
Cons
- More drag / Aerodynamics not as good.
- Less effective as flaps.
You say you're designing a utility/sport jet and you'd like to keep things simple. I would go the flaperon route if I was you. You want to be able to produce the most slop free installation (flutter isn't fun) so you shouldn't even consider a 2 servo wing that has separate ailerons/flaps. You can't beat flaperons for simplicity and low cost. I wouldn't worry about stability because a rectangular planform would stall first at the root even with flaperons.
Since you're using a thick airfoil I wouldn't expect a great increase in performance (read: reduction in stall speed) while using flaperons because: a) plain flaps are not really effective, b) you can't lower them all the way (say 30 deg max).
The 2/3 Flap, 1/3 Aileron proportion is good. Look at some GA airplanes, you'll see that these are the proportions they use. You'll be surprised at how little ailerons you actually need.
4" on a 15" chord sounds very large to me. Be sure to counter balance your surfaces and make sure you use good quality linkages. At the speeds jets fly large surfaces can be a liability IMO.
In a small UAV we're building in my university we're using flaperons as well. We could'nt find any reason to install separate ail/flaps as we have a very long runway to use
It all boils down to simplicity vs. performance. You can expect a marked difference between the two setups in both categories. What you really need to do is decide what's more important for you.
Good luck and keep us posted.