The one major thing about the changing of hands is as was stated, it's like when Nintendo and The Pokemon Company took over the Pokemon TCG from Wizards.
The major differences is that all the old UDE (Upper Deck Entertainment) Printed cards probably won't be banned. If they did, there would be a massive backlash, and the game would die outright.
The real big thing though is that KDE (Konami Digital Entertainment) is taking over ALL aspects, including OP (Organized Play), as in Tournaments. If they follow the OCG (Official Card Game, Japan and Asia) Model for tournament structure, then the only tournaments will be Locals with 2-3 big tournaments in a single year (not counting Worlds) as opposed to Regionals at least almost every month and the SJC (Shonen Jump Championship) circuit all leading up to Nationals and Worlds.
If Konami gets rid of OP as is currently is, the game is as good as dead. The Regionals and (mainly) SJCs are what keep the game alive thanks to the prize support and such.
The current situation is that (outside of Florida) all currently planned and scheduled regionals will still happen since the space has already been rented and such, and Shonen Jump San Francisco will still happen. There will just be no Nationals Invites at these thanks to Konami putting everything OP-wise in limbo.
If they manage to keep Organized Play at nearly the same level it currently is, and manage to make the OCG and TCG releases nearly simultaneous, then the game will probably improve. Also, with no rarity changes in the sets, problems like $130
Dark Armed Dragon and $50
Zombie Carrier (Plaguespreader Zombie in the TCG) will hopefully be a thing of the past.
Although...then we'll have to deal with $50+
Stardust Dragon/Buster and other annoying promo cards unless we get sane alternative releases.
All in all, nobody really knows what will come of this as of yet. We need to know what Konami will do, then we'll know what to do.
TL;DR:

, Konami better not get rid of Organized Play,

, if they do the game is dead,

.