It was done to simplify the relationship between the Targaryen characters we see on the show. George was asked this over on "Not A Blog" and the person who asked also responded that they'd asked Bryan Cogman on Twitter and he stated he's been removed.
grrm: I suspect that "Maegor III" was a mistake, though I cannot say for certain. Perhaps a flubbed line, as you suggest. It is true that the Targaryen succession on the series is different than the one in the novels; most notably, the Mad King's father Jaehaerys II was dropped, as was established way back in season one. In much the same way as the Rhoynar have been dropped from the royal titles, "King of Andals and the Rhoynar and the First Men," etc.
These changes were simplifications, however. The books are very complex, but the practical limits of a television series call for a bit more simplicity. Dropping a king or two accomplishes that.
ADragonDemands: Oh yes, I've also been trying to get in touch with Cogman re removing Jaehaerys II, and he actually responded to my question once submitted to a Q&A on a fansite, but I asked "has Jaehaerys II been removed and how does this affect how the Targaryens intermarried with the Baratheons? The Wiki can't draw a full Targaryen family tree until we know that" and his simple answer was "yes, Jaehaerys II has been removed". Ack. I think that's in limbo state until they can figure out the after-effects (i.e. inventing "Viola Redwyne" instead of Egg's fourth son who was a homosexual). Crud.
Not A Blog, Autograph Hounds (comments)
The following interview with Bryan Cogman appears to be the source of ADragonDemands' comment above (It appears to be the same person who asked George above too).
The Dragon Demands: Has King Jaehaerys II officially been removed from the TV-continuity? Maester Aemon in the TV series says that the Mad King was the son of his brother Aegon V, when in the books he was Aegon’s grandson.
Bryan Cogman: Yes, he’s officially out of show canon. In GAME OF THRONES canon, Egg is the Mad King’s father.
Winter is Coming, Ask a GoT Writer: Bryan Cogman on the writing process, Robb and Talisa, and Renly’s peach