The top charges I hear against Musharaf are:
he was a dictator who threw out elected govt
he dismissed iftikhar without undue process
. He mishandled FATA - attacking Pak citizens there
He mishandled FATA - made deal with militants
he allowed firing on lal masjid
Yes, his coup was driven by what I conider evil intent and even though it removed ganja, it still was his biggest mistake.
Iftikhar - there were and are credible complaints against he ex-CJ (his son). Iftikhar did not offer sufficient explanation nor did he stand down for an investigation. Musharraf took this opportunity to remove a thorn in his flesh but let personal hatred get the better of him in how he went abt it (he didn't read the initial reports of lawyer sentiments clearly which is a intelligence failure!) On this, equal blame on both.
FATA - musharraf or anyone else had and has no clear choice or strategy here. When your own army starts surrendering to terrorists, making the deal is the only way to prevent further damage to the nation's infamy. I think Musharraf should not be indicted on this
Lal Masjid - to me Lal Masjid was a test whether Pakistan can become a fully talebanised theocracy such as Iran or Afghanistan. Musharraf did the right thing ultimately there, thus showing the islamic thugs that they cannot take over law & order
On balance, Musharraf deserved to be fired for the coup but the rest of it is his fault
Whatever happened to the emergency he imposed? That was his final nail in the coffin.