I believe they all have their uses and place.
To illustrate, while an F1 race car is fast, it's useless in the city. You're better off riding around in a smart car. A Mercedes is an elegant car, but is useless in a desert environment. You really need to be on a camel.
HTML5 is another tool to add to your arsenal to get a job done and shipped. That is what really counts. If gaming is a hobby, then it may not even matter what you use.
As for 3d, it is intensive/extensive and takes massive amounts of time and resources that I believe most indie gamers just don't have. It's my viewpoint, that unless you have a phenomenal skillset/money and lots of luck, starting and completing a 3d title is very very difficult and slow. There are a lot of bodies along the way to shipping an indie created 3d title. If you can do it, then you are a rare specimen.
Stay nimble and do a 2D game is what I say. Get a sense of how much effort, time and sometimes money this stuff can take to produce, then try your hand at a 3d title.
Again, I think it all depends on what you are trying to do and the market you are attempting to capture with your game.
I think that's the most I've ever written in these forums.
...sip...