I don't think you would have to worry about stagnate R&D, IBM has always been on the bleeding edge of technology in many arenas.
I don't think, however, that a merger of the two (actually three if you count ATI) companies would "squash" Intel. While Intel has done there share of fumbling on past chips, they are no fools when it comes to new technology either. If I am not mistaken, their road map for 23nm process is in place and it would not surprise me if they already have working prototypes.
I also don't think that an IBM/AMD merger would stifle competition, I think it would make it more fierce, as it would force Intel to never rest and that would cause the same to be true for the IBM/AMD.
Just think, if Intel merged with NVidia and IBM merged with AMD/ATI, we would see one stunning battle of the titans for both processors and GPUs.
Now if only someone would come along to challenge Microsoft, we could get a big bucket of popcorn and relax and enjoy the show!
It's fun to speculate, no?