Don't feel like going into a tirade, especially with only thumbs to type on my phone. The short of my perspective is that both the empire and the stormcloaks are organized and led by assholes, each with a few laudable goals and bad methods of trying to reach them.
As for the specific issue of Talos worship, reasons for/against considering him a deity and worthy of worship are irrelevant. Worship is a personal decision. If somebody wants to or doesn't, that's their call to make, not the empire's or the stormcloak's. The state doesn't have the right or the ability to mandate a worldview or particular set of religious convictions. People can and will believe whatever makes sense to them and will worship accordingly, even if their only viable option is to do it in their own home.
With that said, I'm not a fan of either. I can partly sympathize with both and at times find them both reprehensible. Rather than ally with either, I just massacre aldmeri patrols whenever I see them, because those guys are always condescending, threatening assholes towards me who aren't doing anybody any good.