Personally I like the control tyre for many reasons which include parity of an ultimately limiting factor of performance.
What I do not like due to there being no transparency is how the control tyre is developed. We do not know what manufacturer and/or what riders feedback contributes the most to the direction of the tyres. In a sport heavily influenced by behind the scenes politics and sometimes blatant politics the control tyre has not removed Dorna's ability to manipulate the competition.
My personal opinion in 2008 was that when Bridgestone was forced to supply Rossi they had no choice but to develop their tyres for him rather than Ducati who had done the hard yards in conjunction with BS to make the tyre what it was in 2007. Why did they have no choice. Well if Rossi does not win it is not because of any failing of Rossi it is due to a failing of his equipment. Period. Ducati new this, experienced this and subsequently decided to switch to Michelin which was then thwarted by Dorna's control tyre ruling.
I understand why people like the control tyre, and there are very legitimate arguments for it. I don't, mainly for philosophical reasons concerning the racing I watched in my formative years; I don't like the frequent yellow flags in modern car racing either. I think they are getting close now in motogp to where any further developments to make the bikes faster will preclude humans from riding them, so I may have to re-evaluate my position.
I agree about the potential problems with the lack of transparency in tyre development, but without any inside knowledge it looks to me at present that they have developed a fairly middle of the road tyre which suits the majority of the current riders who have ex-250 corner speed riding styles rather than more idiosyncratic/extreme styles; this is obviously not unfair but may contribute further to the current formula being "one -line" as many complain.
Valentino who has usually been the number 1 rider and always on major factory bikes has probably often had development slanted his way, and one would imagine his input was taken note of for the sns tyres for instance, although I am not sure there is any actual proof of this. I don't think this has necessarily been the case in recent years however, and he is definitely not the only one with influence in motogp. Honda for instance have a lot of pull, and it was rumoured that one reason for his dissatisfaction with michelin was that they were slanting their development towards hrc/pedrosa.