Two things here.
One: just because your candidate lost does not mean you were silenced in any way. Indeed if you assume, as you do here, that losing an election means you were silenced then you are arguing to silence people. Different people, sure. But silencing them nonetheless.
Two: because if those specific big states went with something else there is a chance some of their blue electoral college votes may bleed red. Thus it is in their party interest to stick with what they have.
Changing the methods by which CA and NY allocate electors would not have improved Hillary’s vote. So let’s talk about California.
If anything would be changed in CA it is likely Trump would have had electoral college electors for CA. As it stands, according to your argument all those non-Hillary voters are silenced. They might agree with that sentiment, but it wouldn’t be accurate. Indeed from what I’ve heard and read the “State of Jefferson” movement is arguing about that in particular — that CA is ruled by the progressives in the big cities and the rest of the state is ignored and economically taken advantage of.
But as far as the electoral college itself goes, winner takes all is the only way. Though it wasn’t always. It was originally the case that there was no “party ticket”. Everyone who wanted to run for POTUS did so. Whomever received the most votes won POTUS, and whomever received the second most won VPOTUS.
The best reform, IMO, we could do to this process is to return to that system. Think of how the entire landscape would improve. Presidential primaries? Hah. If each party were to nominate a spangle candidate it would really be a contest over who was P vs VP, and neither party would want that.
So we would have a larger field of candidates. In order for one party to get both seats they have to put up two people for POTUS and both would have to come in first and second. That would bring the VP spot back up in election importance. No more “oh and there is the VP candidate”.
Sure, members of the same party wouldn’t run hard against each other (usually) for fear of winning POTUS but causing their other candidate(a) to lose the second slot. Frankly I’d have been happy to see all the Republican and Democrat candidates on stage together. Let them all talk directly to the general election from the start, no wasting time with “the base”.
Would the outcome have been different? Absolutely. Assuming Hillary beat Bernie who beat (insert other Republican candidate here) we’d have Trump and Hillary in office. And that would be fascinating to watch.
In these cases the VP has a vested interest in the POTUS being “successful”, even if opposing parties hold the office. This would tone the rancor down and make a common point that both parties had to sit and work on. This doesn’t work out in Congress because they all go off to their echo chambers, oops I meant “caucuses”.
But a presidential administration would have to work together. A VP who was constantly trashing and opposing the POTUS would likely be roundly trounced in the following cycle. A POTUS who was unable to work with their VP would likely follow a similar route. Though I think people would likely give the POTUS more leeway than the VP.
And with the way electors are generally chosen, it would “break up” some of the blocks. I think it would make the predictive math a lot more difficult- meaning candidates would have to work harder and smarter.
The less populous states will oppose any attempt to lower their standing in the electoral college. And frankly they should. The office of POTUS is not one of the people. It is a head of a collection of governments, and as such should be decided by said governments. Though so, too, should be the Senate — again.