Hi,
I think Arduino is fantastic for getting up and running quickly, however I have to agree that a lot of shields are a bit of a dead end.
A major positive which more than compensates for the layout quirks is that the transition to standalone builds with whatever layout and connectivity you require is super easy and very well supported.
EDIT: Just noticed that this is in suggestions - so yes, better layouts on the entry level boards would be great.
Duane B.