You mix up challenges with progress. The challenge to engineer the best car always was and will be, as long as F1 isn't completely spec'ed (and even then, wind-tunnels and testing-rigs will help teams understand their cars better, and thus find better setup solutions). This challenge is absolutely no different to last year's, or any year before it.
No in-season testing and staff, wind-tunnel and CFD restrictions aren't "progress", and aren't "better" than before. It slows the pace of progress, and these are just cut-cutting measures.
Tyre-management with slicks? Changing of a flap's angle? These aren't any bigger changes than the move to spec Bridgestones, the demise of the V10s, or any other change in rules. The flap-angle change is nearly negligible.
Different wake-signatures? Teams never worried about that, and never will. A team's only interest is to go fast - what the car leaves behind is the OWG's problem. Drivers will be the only ones concerned with the different wake.
But KERS? First of all, the KERS allowed in LMP cars differs greatly from the F1 KERS, and the requirements from the systems are different. Second, these were only rumors, and were strongly denied. Third, the price of KERS was always known to be high - it's just become more of an issue now. KERS' only real challenge is cooling: Regulations for cleaner bodywork also banned most of the devices used to improve cooling, which is a challenge even without hot batteries and an electric engine. Again, though, don't mix up progress with challenge: No cooling-gills is the opposite of progress. KERS is a new, and welcome, addition - but in this neutered form, it doesn't present half the challenge, and doesn't offer a quarter of the advantages it should.
In the end, it's a simple fact: If you ban an object, you delete a bit of progress. In this case, you delete essentially half of what designers were doing in the last years - and instead, force them into a small box of possible designs, which will soon merge into even fewer designs as teams realize which solution is works and which doesn't. Flipups and winglets are just half the story - what about the incredible works of art that were the 2008 main wings? Three- and four-plane front wings, sometimes with twin bridges above - all those simplified into a plain surface with two miniature flaps, one of them adjustable by just six degrees. Wide, low sculpted rear wings, perfectly harmonized with dozens of airflow-conditioners and designed to create a coupling-effect with the diffuser - now crammed into a narrow tower, essentially in the middle of nowhere.
