I believe the days of chain hotels being more consistent and reliable than independent hotels are long gone. These days, with online review sites like Yelp and TripAdvisor, a hotel that doesn't provide a good experience will get called out and lose customers very quickly. I have stayed at many independent and chain hotels, and I can't say that chains have been any better on average. I suppose that with a chain, you have another avenue to complain if there are problems, but that's about it.

Ironically, if TripAdvisor had existed back in the day, maybe Holiday Inn and other chain hotels would not have emerged.

I do believe that it is important to support small businesses, so I sometimes choose an independent hotel/restaurant/shop if all other factors are equal. But it all depends on the type of travel. For a longer leisure trip, I might look for a boutique hotel or B&B, but for a night's stay on a business trip, it will probably be the closest hotel.

To answer OP's question about points, I use the loyalty program run by an OTA (hotels.com). That way, I can get free nights without being tied down to a particular chain. No elite benefits, but those aren't a big deal and I can get some of them from a credit card.