Indies offer interesting designs, and with some small companies, there is potential for input from the buyer and some people like that the individual for which the company is often named might work on your watch.
I admire the work of several independents, but there are also downsides such that I tend to favor larger more recognized brands. With a really small company, depending on how specialized the movement is, parts could become difficult or impossible to obtain if the company goes bankrupt or the main watchmaker/owner dies. If its a very complicated piece, the number of places or people that could service it or make parts for it if necessary is quite limited and the cost would be quite high. Patek, AP, VC have all been around for something roughly 140-260 years depending on the company and they will all work on any watch they have ever made regardless of its age. Its nice to know that if you invest in a high end time piece that the manufacturer will be around to support you with service and parts. Other companies if they are part of larger corporations (Richemont, LVMH, Swatch) have the financial ability to provide long term parts and service availability.
In addition, with lesser known brands there is often a very low resale value, or they can be impossible to sell, except at a fire sale pricing. I know people here often say one should not worry about resale, but for people who tire of watches quickly and like to try different brands it can be very difficult to unload. One pre-owned watch store in my area won't buy anything unless its from Patek, AP, VC, Lange, Rolex, and Cartier. The owner said, yes there are lots of great brands but the market and interest (at least in my region) is so weak for them that he won't even make a low ball offer on other brands.
Each buyer has to decide what is right for himself. Cheers!
A few stats from a not-so-lower-end "independent" - Greubel Forsey.
They've been around for about 10 years, and produce only around 80-100 watches a year. Keep in mind, these are ultra-complicated quadruple tourbillons or specially commissioned pieces that involve microsculptures, and Stephen Forsey says they've been able to move every single piece they've made every year despite the hefty price tag. Might not be your cup of tea given some of their design choices, but it's someone else's cup of tea.
So there are close to a thousand GFs out there given their ten year run. And in that time frame they have only seen THREE GFs come back to them for service. One of those included a piece from a collector in HK who just stopped by a pop-up watch workshop that GF organized; the watchmaker had to kind of beg the collector to take the watch in for service as he identified a few potential items of concern after taking a look.
I'm not sure where the other GFs are kept, if they are even worn, or if they're sitting in vaults somewhere; Stephen Forsey and his team say that they are ready to service any watches sent to them via their dealer network, but they will have to be serviced in Switzerland given the level of complications. And I'm not so sure they are staffed up to handle a "deluge" of GFs to be serviced, if ever that happens.
Just some anecdotes to support @Dino944's thoughts above.