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Basically--all the flops have been niche vehicles. Their main products--Fit, Civic, Accord, Odyssey, TL, MDX, etc--are good vehicles that are doing well.
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I wouldn't call the TL a success Mitlov.
Others already addressed the market success thing. I'd also argue it's a mechanical success, because a TL SH-AWD 6MT offers roughly comparable performance to a 335xi (bigger, true, but more advanced AWD system) for about 80% of the price (assuming similar amenities).
The only area where the TL completely flopped was styling, and that's as subjective as subjective can be.
Also, with the exception of the Odyssey, all of the new Honda offerings have been flops - Insight, CR-Z, CrossTour, ZDX.
New models in 2008, 2009 and 2010 (not just facelifts):
Accord (sedan and coupe)--success
Fit--success
Odyssey--success
TL--success
CR-Z--failure
Insight--failure
CrossTour--failure
ZDX--failure
We have four successful bread-and-butter models and four failed niche models. They admittedly need to do fewer niche models but put more love and thought into each one, but overall, it's hardly a picture of a company that's failing in everything they try.
Where is the innovation that used to be based on excellent engineering?
First and foremost: torque-vectoring AWD, which is now sweeping the luxury brands (BMW, Audi, Saab), was an Acura innovation in 2005 (on the RL), if I recall correctly.
Name another inexpensive piston-driven performance car that can comfortably rev to 8000 rpm. The next car that I'm aware of that can do this is the M3, which is more than twice the price of my Si.
They've got some pretty sophisticated cylinder deactivation on the Odyssey. They're not the only company doing that, but my understanding is that the Odyssey's system works pretty seamlessly.
The Fit magic seat. Hell, everything about how that car is packaged. Not since I watched Dr. Who have I seen something that's so much bigger on the inside than the outside.
Their manual-transmissions (which are still arguably the best-shifting on the market) may not be "innovation," but they're sure as hell good engineering.
I'm sure if I scratched my head I could think of more. But I must emphasize that you don't have to invent an all-new technology (like VTEC) every three years to have "good engineering."