If they are going to bring 5Ds to Duel Links they should separate the series from DM and GX for example: Characters in DM and GX CANNOT use Turner and Synchro Monsters since they never existed in previous series. Also playing a DM or GX character in PVP, you only duel against players who use DM or GX characters and not 5Ds characters. All this makes sense because 5Ds takes place in the future. If there is an event where time traveling is involved, then that's fine but DM and GX characters still can't use Turner and Synchro Monsters. I am not really a big fan of 5Ds but I'm still looking forward to it.
I'm not a fan of 5Ds neither, for me they could just ignore this series until at least they complete the roster of DM and GX. I also agree with your comments about the characters being separate from each other, it totally makes sense. But my guess is that Konami won't make it this way, so prepare to get angry.
Locking characters out of an entire summoning mechanic wouldn't be fair to the fans of those characters who'd want to make use of the mechanic. If anything they might be able to throw Synchro haters the bone of introducing a new mode of ranked play which doesn't permit Synchro summoning.