I don't think it's as black and white as that. 2010 Djokovic is not winning the AO over 2004 Federer, for example, and I don't think 2009 Federer is winning Wimbledon over 2015 Djokovic. So they might split Slams but it would be more or less across the board.
Well if you want to put it like that...
AO:
04 v 10 Federer, 05 v 11 Djokovic, 05 v 12 Djokovic, 07 v 13 Federer, 08 v 14 Djokovic, 09 v 15 even, 10 v 16 Djokovic. Total 4-2 Djokovic.
RG:
04 v 10 too weak to consider, 05 v 11 even, 06 v 12 Federer, 07 v 13 Djokovic, 08 v 14 Djokovic, 09 v 15 lean Federer but let's play nice and call it even, 10 v 16 Djokovic. Total 3-1 Djokovic.
WB:
04 v 10 Federer, 05 v 11 Federer, 06 v 12 Federer, 07 v 13 Federer, 08 v 14 Federer, 09 v 15 Djokovic, 10 v 16 too weak to consider. Total 5-1 Federer.
USO:
04 v 10 Federer, 05 v 11 playing nice to call it even, 06 v 12 Federer, 07 v 13 Federer, 08 v 14 Federer, 09 v 15 Djokovic, 10 v 16 even. Total 4-1 Federer.
Grand Total 12-9 Federer. Modest edge as I said.
Actually I've never done this before so let's try it for the whole careers:
01-03 v 07-09:
AO:
01 v 07 too weak to consider, 02 v 08 Djokovic, 03 v 09 too weak to consider
RG:
01 v 07 Djokovic, 02 v 08 Djokovic, 03 v 09 too weak to consider
WB:
01 v 07 unclear / too weak, 02 v 08 too weak to consider LOL, 03 v 09 Federer
USO:
01 v 07 Djokovic, 02 v 08 Djokovic, 03 v 09 Djokovic
Grand Total 6-1; I think RG 07 & USO 09 could be argued below slam-winning level for Djokovic against a medium level opponent though, he lost to Fedal but not that close (09 looks closeish score-wise but Federer strongly controlled play in the last two sets, kind of lazy not to break earlier). So it could be penciled as 4-1 too. Let's shave off 07 RG and put it at 5-1 then. After all, Ljubicic technically played a closer semi vs Nadal in 06 and no one half-sane would consider him relevant at the highest level.
11-15 vs 17-21:
AO:
11 v 17 Federer, 12 v 18 Federer, 13 v 19 Djokovic, 14 v 20 Djokovic, 15 v 21 Djokovic. Total 3-2 Djokovic.
RG:
11 v 17 Federer, 12 v 18 too weak to consider (see, Federer did reach SF but I'm ignoring it because his level wasn't up there), 13 v 19 Djokovic, 14 v 20 too weak (not rating this abomination of a final performance same as Federer's 08 clownery), 15 v 21 Djokovic. Total 2-1 Djokovic.
WB:
11 v 17 not considering (obviously Federer but not even creating a BP in 4.5 sets is plain sukk however good your opponent is), 12 v 18 Federer, 13 v 19 Djokovic, 14/15 vs 21 edge Federer (counting both against 21 due to the absence of 20 WB and I say Federer looked better against an equal or better non-Djokovic field than Djokovic in 21). Total 3-1 Federer.
USO:
11 v 17 Federer, 12 v 18 Djokovic, 13 v 19 too weak to consider, 14 v 20 N/A, 15 v 21 Federer (much more dominant against the non-Djokovic field uincluding Wawrinka and pushed Peakovic close). Total 2-1 Federer.
Grand Total 8-7 Federer.
The full total is then 1-5 + 12-9 + 8-7 which yields an even 21-21, somewhat unexpectedly. Federer with the better peak/prime still but going into the sub-levels, assuming they are still good enough to win against average competition at that stage and thus relevant in the dicussion of slam-winning levels, brings them close. Djokovic timed his levels somewhat better regarding the competition as Federer's losing levels are generally higher than Djokovic's (all those close five-setters and four-setters, yeesh).
It'd be pretty boring otherwise.
