According to the Air Force website the F-22 can carry 2 1000 lbs JDAMS in the ground attack mode. The F-15E can carry many more and at a fraction of the cost of an F-22. Boeing has upgraded the design to make it stealthier than older models, though not as stealthy as the F-22 it could certainly improve survivability. A mix of F-22s for air superiority and new, upgraded existing designs would be a more cost-effective solution to the F-35.
You are correct in saying the Raptor can only carry 2 1000 pound JDAMs ....however it can also carry 8 GBU39 Small Diameter Bombs, which are smaller than the 1kJDAMs, but have wings that enable them to glide long distances (which coupled with a supercruise launch from a Raptor enables them to go far). As for making F15s stealthy ....the Silent Eagle concept is a half-joke. The RCS for a F15 is 25m2, as compared to that of a Raptor of 0.0001m2: they are not only compatible, but fact is one cannot make the F15 stealthy enough. Not even against X band radar ....and against L and S band even the F35 would have problems. Also, the internal carriage of the F15SE in the conformal tanks takes space for fuel. Anyways, against a third world country the SE is ok, but against an advanced IADs the Raptor makes a world of difference.
First off, you only quote the internal capability of the F-22. Yes, only two 1000 lb GBU-32s. But the F-22 has four external hard points capable of 5000 lbs. That's 22,000 lbs of bombs plus it can still carry two AIM-120s and two AIM-9s. (For comparison, the F-15E can carry 24,000 lbs of ordnance total.)
That's the capability aspect. The F-22 can do everything the F-15E can do, but the not even close the other way around. Your second point was cost. Well, we know the fly away cost of more F-22s: $140 million. The cost of the latest F-15 is $100 million according to Boeing. The F-35 is not known, with estimates between $85 and $210 million each. I dunno, but I think that the F-22 is reasonably priced since it can do the job of both the F-15E and F-35, plus jobs neither of those planes can do.