With the smaller chambers of the 2.5L, the 3L valves already have to be unshrouded when we use them on a hybrid 3L. Since yours will be used on a 2.5L where deshrouding the chambers can't happen (to the extent needed due to the smaller cylinders), I would say stick with the stock sized intake valves. Exhaust valves would be a nice experiment though...
What really matters on your 2.5L is: "Where is the restriction?" With the stock SE intake manifolds on the engine, the restriction isn't really in the heads anyway, it's the intake manifold, exhaust manifolds, and restrictive single exhaust. You've mentioned a better single exhaust, which is a good start, but unless you also plan on headers and an SVT (or better) intake setup, the extensive head work will be a big waste of time IMO. Leave it at a general cleanup and remove casting flash where needed unless you are investing or plan to invest in the above.
Keep the deck as thick as possible and only mill enough to clean up any surface imperfections. If you want compression, do it right with new pistons and leave the quench area alone on the heads.
