It is just that when it comes to the F-15 Silent Eagle there are some aspects that are quite evident in terms of showing it is a superlative fighter, for instance its flawless combat record. The F-15 base that the SE would stem from is really an amazing platform.
However, there are also a couple of questions that arise when one looks at the SE from a 'stealthy' perspective. For one, the base model F-15 is one of the least stealthy platforms currently flying from an RCS perspective. According to white paper sources its RCS can be a high as 20m2, as comparable to a Eurofighter at 0.5-1m2. Obviously RCS figures are not everything, but when the F-15 was being designed there were other more important metrics that were being sought after, which the Eagle met, and lowering RCS was never a factor. Even in the limited way that somehow lowering RCS was during the design of the Hornet/SuperHornet. Thus, using that as a base for a stealthy platform does raise some questions, especially compared to designs that are set up from the first go as stealthy. For instance, the YF-22/F-22 platform has stealthy attributes even without RAM application. The very shaping of the design incorporates stealthy ideas. The shaping design of the F-15 incorporates large air-intakes, interesting angles, etc. Now, I know in the SE the vertical stabilizers will be canted in a V-shape similar to the Superhornets (and F-35/22), and that it will have a radar blocker in front of the fan blades (similar to what the YF-23 had and the PakFa may have). I wonder how they will work around the variable geometry inlets, since that appears to be a potential re-design issue.
And talking about RAM, the SE will have copious amounts of RAM based on the 2009 tests. Maintenance will thus have to be a major consideration, especially considering that this is a fighter plane and not a subsonic bomber. However, I am sure this is mitigated by recent developments in RAM application and maintenance techniques.
Anyways, I am obviously not part of the design team for the F-15SE, and thus I am not privy to the answers they may have come up to some of this issues. It is also obvious that they MUST have come up with answers (I am not one of those FReepers who assume the designers are incompetent ...e.g. I remember when the PakFa came out two FReepers kept saying it is 'useless' because it has a canopy that has metal supports, ignoring the fact that the F-35 has the same, as does the YF-23 that was alleged to be stealthier than the YF-22). But I digress.
Obviously I don't have any real info, but just from a layman's perspective the base F-15 design was not the best starting point for a stealthy platform, even though as a fighter platform it is definitely amazing (the Eagle design evolutions like the F-15K for South Korea and F-15SG for Singapore are still competitive against newer designs like the Eurofighter and the Rafale). It may be possible that it is one of those trade-off exercises that brought forth discussions like 'is it better to design a fighter into a ground-attack plane, or a ground-attack plane into a fighter?' The answer to that was shown to be converting a fighter into an air-to-mud (e.g. F-15C to F-15E) was better than the inverse. Thus, maybe it is the same thing here ...that converting a fighter platform into a stealth platform is easier than meeting the costs required to convert the F-35, which should really be called the A-35, into a superlative fighter when it comes to facing off against next generation threats. That might be the angle Boeing is aiming for here, and why they chose the F-15 - a proven platform as a fighter AND multi-role - as their base for the 'stealthier version.'
I've also read their claim that the SE will be as stealthy as the F-35 in the forward hemisphere. That I have a hard time believing, unless there is something REALLY WRONG with the F-35 from a stealthiness perspective. Even with all the problems the F-35 has experienced, it should still be stealthier than a F-15 with a canted tail, RAM overdose, and fan-blockers! Especially considering the F-35 was designed from scratch to be stealthy from a RCS design perspective, as well as having RAM also. If the SE is as stealthy as the F-35 from a forward angle, as claimed, then the other claim of the F-35 having an RCS of 0.001 m2 is definitely questionable. One party is lying ...either Boeing with their claim of RCS equivalence to the F-35, or Lockmart with their claim of 0.001m2 RCS (maybe both are lying).
Boeing has experience in making major RCS reductions with a little reshaping and strategic placement of RAM when they designed the F/A-18E/F.
The Eurofighter isn't very stealthy when fully loaded with external stores, and neither is the F-15. The key to the F-15SE's stealthiness is the redesigned conformal fuel tanks that can carry a couple of missiles internally.
The biggest advantage the F-15S has over the Eurofighter and the F-35 is that South Korea already operates the F-15K so infrastructure costs would be much lower.