Er... I think we need to clarify exactly what a game "Engine" is. It's the underlying software that is used to make a game, to draw a loose analogy, like the MS Word that makes your documents, or the Photoshop that makes your pics.
In this regard, it's not an issue of engine reuse at all, but rather shoddy development. Even if a brand new engine is used for each game, the games produced would still stink. Nobody's going to care that effort went into making new engines, they just see the end product and think "bad game".
Effort is never a judging criteria, period. You can argue about how this company took this many years to develop this or that, but if it still turns out bad or mediocre, all that effort isn't going to count for anything.
Looking at pokemon, it's actually a huge example of the same thing over and over. Across all 5 generations, Gamefreak hasn't made any radical changes (a "radical" change is not something like physical/special split, it's something that can cause one Gen to be so different it's like comparing Mystery Dungeon with Ranger).
The core aspect is still there, they just added more cake icing and change some icing each generation (eg. battle subway instead of Tower).
And it works. Nobody (excluding whinies) complains that Gen V isn't unique or innovative in general, or that the plotlines need to improve or the gameplay needs to be more unique beyond the same turn-based brawling since Gen I. And one major point is: nobody complains that Gamefreak doesn't fully develop the first two games each gen and choose to cash in on a 3rd game with more features. It really is all a perspective issue, whether one convinces himself to see something in a positive or negative light.