As the now proud owner of both Deities and Demigods and now the Epic Level Handbook.(And I bought them both).I wuld say that I don't have a problem with the way they did it.
This is not a case of the left hand not knowing what the right hand was doing and think the decisions were well thought out and hard choices were made about what to do about the differences between the 2 books.Here are a few of the problems they had to deal with.
Their rule about not requiring any other books than the 3 core books to be able to use the majority of the info in a new book unless it is a setting supplement in which case the Setting corebook is also needed.
The books serve different purposes the D&Dg bood is mainly for DMs and stats out gods beings that the PC's worship and are unlikely to ever meet in a regular(non-epic)campaign.ELH on the other hand is meant for players(and DMs) for creating very high level PC's.If you didn't know the other one existed, you would be happy.
If they had included Epic stats in the D&Dg book how would they handle it seems to me they had 4 choices:
1.Just include epic stats and magic items,don't explain them other than to say look them up in the upcoming ELH.(you think they are getting complaints now)
2.Include the epic stats,along with a mini 4-6 page explanation of them.This of course opens a whole new can of worms.First which deities get removed to make room for info they will be printing again in three months and How many sales of Epic level handbooks do they lose because all someone wanted was what was on those six pages(most likely feats).
3.Include a brief section on how to convert to epic level in either book.Again you are left with what gets removed to make room for this new info.
4.And of course they could keep the books totally separate which is what they choose.
One does need to keep in mind that the D&Dg did come out before ELH (albeit only 3 months before) and they shouldn't be expected to have info from future products in them.
I think the more interesting question at this point however is what about the future.Is ELH a one time shot that will be quickly forgotten by WoTC even if they do eventually make it OGC.Or will we see regular references to it in upcoming products after all it is not one of the three core rulebooks but it is the closest so far to being so.
I find it interesting that ELH does include some Psionics Handbook related stuff sure if you don't have PsH you could skip over it without to much of a loss.But it is in there which gives hope to ELH stuff being included in the future.
My main intrest is with the upcoming MM2 and BoVD will they include Epic stats especially in the BoVD will the Fiendlords have epic stats.
I guess they can handle The fiendlords in one of three ways.They can give them MM stats,D&Dg stats or Epic stats.My personal preference would be Epic after all if any one takes on Orcus,Demegorgon or Asmodeous and they aren't Epic level I don't think they stand a chance and if the characters have Epic stats well don't you think the fiends should to

r the could take the route of making them minor(or major) deities(especially since many of them already have worshippers.)But most likely they will take the MM route making them not a whole lot more powerful than say a red great wyrm.
An interesting question then becomes when does a rule(s) become so important to a changing evolving game that it needs to be added to the core rules.and when that happens what do they do.
1.4th edition(noooo!!)
2.Players handbook II-corebook 4(official)
3.New updated players handbook with new chapter.
4.Do nothing just keep explaining new rules in every supplement that uses them.
1st edition took choice 2 in that they were always coming out with new official stuff them most recent being the gospel.
2nd edition took choice 4 and expalined the new stuff in every book the biggest example being kits they are never once mentioned in any of the core books they were then introduced in the fighters handbook and they appeared everywhere after that I think eventually they stopped expaining what they were simply because everyone just understood.They were the core rule that wasn't in the corerulebooks.