I'm thinking in the end capturing the booster will go to a controlled/soft water landing and tow it to the harbor - some things are the way they are just because they work
I'm thinking that the days of NASA deciding who does what in space are numbered - and short
SpaceX has repeated tried to recover their boosters from water landings. Based on their experiences with those attempts, they've decided to pursue this "fly back to land" approach. Note that while they currently recover their orbital Dragon craft via water landing, they would also like to transition that to a land-based recovery as well, for similar reasons.
Re: NASA, that may be true. But regardless of what you think about NASA, they're the only reason SpaceX exists right now. SpaceX could not have gotten the investors or commercial customers needed to "get off the ground" without first the seed money and then the contracts that NASA awarded them--that gave them the legitimacy to draw in the rest. Plus the $1.6B from their contracts to deliver cargo to ISS currently dwarfs all their other launch contracts combined.
They also used numerous bits of the body of research that NASA has compiled over the decades in their booster and orbital vehicle development. They didn't start with a blank sheet of paper and do all their development in a vacuum. In short, they would not be who they are without NASA.
As for the future...
Today, "civil commercial space" = "launching communications and earth-observation satellites", plus the new and tiny role of SpaceX and Orbital in launching cargo to ISS.
Tomorrow and for the foreseeable future, "civil commercial space" = "launching communications and earth observation satellites", plus the new and tiny role of SpaceX and Orbital in launching cargo to ISS, plus possibly resuming the launch of US astronauts to the ISS in a few more years.
Beyond that, there ain't nuthin' new happening "soon", and nuthin' new's gonna happen until someone...maybe SpaceX, maybe someone else...figures out how to make a buck out of it.
Virgin Galactic's trying to create a business around selling rides into space on their SpaceShipTwo, but they've been working on that for over 15 years now, so I guess it depends on what you mean by "soon" and how game-changing you believe that commercial venture to be re: NASA's future.