Governor vs speaker and the political questions

the Karnataka crisis has thrown some serious  questions over the current political dispensation, the crisis emerged when 11 of BJP and 5 independent members withdrew the support from Yeduyarappa govt leading to almost fall of the razor thin majority govt, but issue of a sort of warning by the governer to speaker of the house on the eve of the test of strength, not to disqualify any member under anti defection act and allow them to vote but during the test the rebel members were disqualified by speaker which led to reducing the effective strength of the house itself in which BJP managed to win the majority. in between governer hastily recommended the imposition of president rule.
                                                           rebel challenged the decision of speaker in the high court, two member bench gave the split verdict one supporting other opposing the speaker decision.now it is refer to third judge.

whatever be the decision of the court but the real questions are much larger than that be decided by the courts,like what is the real power and what is the limitation of discretion of governor,how far it is logical that governor keep working as an agent of central government when the evidence suggests that he\she often end up becoming a political agent of the ruling party at the center,in what circumstances he must refer the case for president rule,is his personal or subjective assessment enough for the case?can he issue directives to the speaker of the house about conducting the business within the house?
can speaker be immune from the advises sent by governor? who has right to decide what should happen with rebel? the question of politicisation of speaker himself since he also belongs to a certain political party, should the anti defection law be applied blatantly leaving no room for political dissension!
there are many answer to these questions that are suggested by the experts like giving practical shape to the reports of the sarkaria commission in latter and spirit to depoliticize the office of governor, following the rule laid down by supreme court in bommai case in the matter of power of governor to dissolve the house like individual may be personally responsible to the governor but govt has to show collective responsibility to the house,supreme court directives that speaker decision can be challenged in courts in the matter of defection etc.
the real issue is that these problems are going to gravitate in near future, because the trend in indian polity suggests so. coalition government at the centre is likely to stay in coming future which means small parties would like to yield more power through influencing the agencies which are supposed to remain neutral from political influences. most likely party at the helm of affair in state and at centre would be different so the tendency of interfernce by the party at centre in the matter of state would be higher.
the above questions posed above need to answered keeping in the mind the future trend in indian polity and vulnerability of indian politics.