Some libraries may have to be tweaked anyway .........
This is definately true!
Usually you may also not find serious error handling, an absolute 'no go' for reliable software, but tolerable for hobby applications.
That what Arduino was designed for!
Defining a new GPIO-Pinout will not prevent users selecting boards like the mosquino.
If users share there tweakened libs with the cummunity, mosquino will be an serious tool.
But why not use it with AVR-Studio and some reliable and tested libraries/drivers for the ATMega family ....
The Arduino Software was never intended for use in commercial/critical projects!
The 'three port' solution that mosquino uses, allows als an dedicated shield for debugging porposes via the JTAG Interface if this is necessary.
And .... evolutionary changes of technical concepts will usually bring some benefit for the user or software developer 