...why should V have a connection with the bad guys? And you have a reason to attack Smasher IF you want one. Otherwise, he is just an obstacle for our hero to overcome and I don't see the problem with that.
So a game where a mercenary (not this one, although it can be I suppose) is hired to do something, is not really about them, but about their employer?
The reason there should be a connection is because it makes for a better story and more believable protagonist that one can relate to. Lets imagine that V and Jackie were hanging out at a bar together and suddenly Arasaka soldiers and Smasher shows up, because they have to do some mission there and they are being real bastards, during that Jackie is executed by Smasher, because he means nothing to him or whatever. V only makes it by pure luck... or whatever.
Now you have a reason or motivation for why V is angry at Arasaka and Smasher. You as a player can understand why V is upset as they wronged you and murdered your friend for no reason. At this point you could throw all of the Silverhand in as well, it wouldn't change that V still have a good reason for why he/she want revenge and is not written out of the story.
But as I said, as the story is now, V and Jackie are the ones that are being bastards against Arasaka and kills a lot of innocent people, regardless of what is going on internally with them. Smasher is just some famous bodyguard and is not even the one that kills Jackie.
The only motivation or connection that could potentially be there in this setup, is that Arasaka tries to blame V and Jackie for something that they didn't do, meaning killing the father, but that is not used as a driving force in the game, its not about clearing your name or Arasaka hunting you down or anything, because as V you are going to die anyway so it doesn't matter.
Dexter which could also be a motivation for V, is also taken out of the game almost instantly and forgotten, so he is not relevant either.
So what you are left with is just some random person running around doing random missions for no reason, helping a terrorist stuck in their head, which also doesn't have a good reason/motivation for what he is doing, but that is sort of what you are left with. So adding it all together, the story is just not very good, because it doesn't manage to give you a reason to feel sympathy or why you as a player should really care about what is going on, because the connection between V and the bad guys doesn't exist.
The main plot in my opinion, might as well have been a random mission. Where you get a mission goal, do it and then forget about it and move on to the next one.