:I find it continually challenging to know how to respond to this sort of issue. In Tibet, the Geshe studies were undertaken over 20-40 years, with upwards of 50 months per annual cohort finishing the degree, taught at various monasteries of different schools, since the 12th Century CE. One of the five masteries is Madhyamaka. Every single academic studied this for a minimum of 3 years, normally much longer. They would be expected to read hundreds of scholarly commentaries based on this. One major branch of academic study arose via the works of Je Tsongkhapa. So we have hundreds of years, with hundreds of thousands of monks debating on every single nuance of his works, (and a whole load of other authors too).  The depth of the analysis is incredibly hard to get to grips with, unless one is willing to spend a similar amount of time studying it. So, nowadays we see these arguments having been transferred over into the Western academic sphere -  for example, read Garfield's "The Conventional Status of Reflexive Awareness: What’s at Stake in a Tibetan Debate" ; a direct response to Williams 'The Reflexive Nature of Awareness' where William promotes one of Mipham's criticisms against Tsongkhapa.    
 :So, what I am saying is that when we look at this material, it's not a criticism of Tsongkhapa - it's a scholarly debate involved in examining Tsongkhapa's works and, in general, limits itself to the narrow field of Madhyamaka studies within a Geshe curriculum.  As such, this isn't a criticism of Tsongkhapa, (even if sometimes the language gets florid). There are criticisms of Tsongkhapa, based on whether or not he needed to start a new school - whether or not he was able to live up to his own high standards, etc. (for instance, Drukpa Kunley's critique - that TK never met the common man, but spent his time as a recluse- find your own source for this, mine was via oral tradition).    
 :In brief, if the best scholars of East and West, over the last 600 years, cannot come to a conclusion about Je Tsongkhapa, we are foolish to take sides on this sort of thing, especially as every Buddhist teacher, from the first, tells us to 'find out for ourselves'. One thing that we can be sure about, is that Je Tsonkhapa's views were worthy of discussion!  (  )