Eh i prefer it that way actually. The best Episode featuring them was Dalek in the first Season of the Reboot. Given that there was alot of exposition on the Time War and a interesting dialogue between the Dalek and the Doctor. As well as a neat ending to it when both sides realized how they changed. The Ending to the first Season also worked, i.e. a last Battle of the Time War where both sides were virtually wiped out, except for the Doctor and as we learn later, the Cult of Skaro, which i liked as Villians as they were few in Number and being able to think like the Enemy, which made them a bigger Threat than the Emperor and later Davros and his Empire.
Also showed some interesting development away from "We kill everything". I.e. Sec and Caan changing, the latter ultimately destroying his own Race by manipulating the Doctor to do so, in a manner of speaking. When they were brought back in Season 5 i actually thought "Not again", given that they were now back to their usual Self and again somehow survived when it was made clear that they should be destroyed for good. Though the Cliffhanger Ending worked as they were remade into a more powerful, pre-time war Race. Hence by any definition the Doctor doesnt stand much of a chance against them right now, at least he wouldnt be able to defeat them without killing himself, as was shown in that Episode.
I'd actually prefer they go after other Storythreads, i.e. the Silence, whoever was behind the Silence because, lets face it. They may be devious and manipulative, but they have nowhere near the Power to destroy a Tardis or manipulate it to become stuck in the first place. Which means someone else was behind this. And im still hoping that it was Omega. For those that dont know, Omega is one of the Founders of the Time Lords and the only other surviving Time Lord in Existence given that he actually lives in a Anti-Matter Universe, hence he would technically be capable of influencing the TIme Lord Technology and such.
There is also that single part left open with Jenny, ya know, the Doctor's Daughter, who may make a re-appearance at some Point in time, potentially surviving Time Lords, as i doubt they would re-use the Master again after the Christmas Specials where he was not only "destroyed" but also time-locked as he forced Rassilon back into the Time War, along with himself. Hence instead of re-using older Enemies like the Daleks and arguably the Cybermen, they should rather focus on new Enemies like the Silence and potential surviving Time Lords, like the Rani for example, or as i hope, Omega. As he would be a very interesting "Big Bad Guy" Type of Enemy for the Doctor.
