Lack of advertising, investing in the wrong people, lack of attention on home-grown wrestlers for wrestlers from other companies (though some wrestlers are an exception), and general mismanagement.
Among other things, when TNA attempted to enter a 'Wars' with WWE, that failed miserably in TNA's favor (it was way too early), and once they started bringing in all the WCW (The Band, Immortal) and ECW (EV2) guys, it began to hurt rather than help since it promoted ECW and WCW more than it promoted TNA, especially when they started to get rid of the things that made them stand out to be more to essentially feel like a WWE 2.0.
Lack of Money
-- despite Panda's deep pockets, they keep the wallet pretty tight for TNA
Lack of clear Vision
-- Jarrett knowing he was the one guy who'd never leave with the Belt never let the belt get too far away from him for the first 5 year
Lack of Identity
-- for most of TNA's 13 years they have either been WCW-Lite, ECW-Lite, WWE-Lite... for a sweet tiny portion they were actually 'TNA'
Lack of a real name...
-- FFS they called themselves TNA with a straight face
not enough money and awful booking, plain and simple
