Even though Republicans control all branches of government, in order to get any real legislation passed they still need support from 8 Democrats/Independents in the Senate to avoid a fillibuster, barring any changes to the Senate rules. They were able to identify a workaround through the budget reconciliation process, and developed a multi-stage plan in order to enact as much of their desired policies as possible without assuming any Democratic support.
The first part of that plan has failed, and has called into question the entire proposed process. Now it seems likely that the Republicans must try to engage with Democrats in order to get any legislation passed, which is a tall order from all sides in the current political climate. It is a blow to those further to the right politically, many of which President Trump has embraced, since Democrats in the Senate will (in all likelihood) now be included more in national discussions and legislation can begin to move forward under this administration.
Alternatively, entrenched positions could become more entrenched, and the status quo continues, though Trump has signaled that he really just wants to move forward and save as much face as he can. His public statements are to just let the healthcare industry implode, but as a President that is not a politically viable option so "deal making" maybe will still have a chance to happen, if and when improvements to the current system can be identified, proposed and debated, but the Big Deal™ is that Obamacare survives (for now) during a time of Republican control after years of not only talking about repealing it from the ground up but actually voting to do it when it didn't really matter.
When it did matter, they failed to actually come to an agreement among themselves on exactly what they wanted to do differently. Now, any future legislation on healthcare cannot happen under the budget reconciliation process. Unless Republicans can pick up 8 more Senate seats in the midterms (which is not impossible), they must secure additional votes from Democrats who are unlikely to support much without significant concessions. Historically, midterms are more a referendum on the sitting President, with their party generally losing more than winning, and Republicans shouldn't bet on getting a chance to do a re-do. Moreover, hard feelings about the process may persist, which could impact negotiations in other big landmark legislation such as tax reform.
This all assumes the filibuster survives until then. Ultimately, though, I feel this is a bigger blow for Paul Ryan, since his persona is more as the Republican's deep policy idea pusher, and this was more or less his healthcare plan. Trump himself has proved to be fairly slippery with regards to personal responsibility.