It sounds like it'd be better to update them together, but I think Riot is doing them separate for a reason & I think I know why.
(These are just my opinions, I could be entirely wrong).
[Runes Reforged]: Runes/Masteries were a very important aspect/mechanic in League. With Runes Reforged, they introduced all new mechanics (Kleptomancy & Summoners Spellbook are great examples) to the game that players will have to play around. It would make sense that they hard focus on making sure that** ALL** the runes are in working order & that champions are properly toned down or beefed up to compensate for this major change.
[AP Itemization]: While the AP Items are in _DIRE _ need of work, Runes Reforged was a major project that took Riot's Dev team possibly a year (Give or take) to finish. So my guess here is that they figured they could hold off on AP Items for now & get the big project done first. I imagine that the AP itemization will include number changes, a few item reworks (Rabadon's Deathcap
& possibly Rylai's Crystal Scepter
) & possibly 2-3 new items.