When you compare AMD and Intel, its actually Intel making huge mistakes, the amount of truly crap Atom's they've made, and Itanium, the R&D costs alone for those two projects likely dwarf AMD's R&D budget for the past decade.
AMD's biggest problem is a world of increasingly difficult to make, increasingly expensive processes, IE it used to cost say half a billion to bring in 90nm, a billion for 65nm, 2 billion for 45nm, 4 billion for 32nm, 6 billion, etc, etc. While the AMD never had the cash or volume to compete. 4billion on a process you can put in 5 different fabs that can supply 90% of the market for Intel, 4billion for AMD to put in 1(2 fabs depending on what you call them) for 15-20% of the market tops... and then having such a massively smaller R&D budget that the chance of having better CPU's is none, only when Intel screw up massively is it possible. Unless AMD could charge 2-3x what Intel could, there was no way the ever increasing process/shrinking costs would work out on the volume AMD produced.
Likewise with margins shrinking on chips, expanding to new markets is the way the best sillicon companies will survive, but Intel are having next to no impact with Atom because, it sucks, and costs a crapload... AMD have the same challenge but 1/50th of the R&D budget and 1/100000th of the cash on hand to push into the market, buying contracts, marketing, everything else that can push a product from loss to profit.
People see the ATi aquisition as overpriced, because the value plumetted, but first no one else saw the market crash and second, at 1billion 3 years later, with banks/financing not remotely possible AMD couldn't have afforded 1billion after the market crashed, without ATi and graphics, AMD could quite easily be completely dead by now.
AMD have made mistakes, but most of what has happened to them has simply been the situation, when AMD were the best, Intel were using decades of profits to pay people not to buy their chips, had that not happened, AMD made killer profits for a couple years and invested that in another fab and massively increasing their volume, everything COULD be different, at worst they would have gotten a far far better deal when they sold off the fabs.
Intel makes mistakes that financially make AMD look like a ridiculously well run company in comparison, their overall size and the ability to eat those losses are the difference between the companies. Intel can make a 3billion screw up, and a CEO gets fired and the board get slightly less big bonuses that year, AMD make a 300million screw up and the company balances on the edge of collapse.
Where AMD go from here, who knows, Microsoft, Intel, AMD, the x86 trio all really need to come up with a "new" format to compete with ARM, so much legacy crap, so much overhead and waste that ARM doesn't have(but will in a decade or two). If Intel/AMD remove the bloat by making a new instruction set and moving on, gaining power efficiency they might make a real fight of tablets/ultra portables and even phones. With x86 there is no chance they can take make any inroads in those markets.
MS need a OS from scratch, or Intel/AMD and Nvidia need to jump on the linux bandwagon, get game dev's to completely ditch Direct X and move to a streamlined OS again without the terrible bloat.