The Ultimate Collection
 

So issue 1 of this series collects comics 1-7 and the Raphael one-shot, issue 2 gives us comics 8-11 plus the Donatello, Michelangelo and Leonardo one-shots - all is well up to this point - and then issue 3 starts to skip stuff, like comics 13 and 16 and 18.
Issue 4 launches us WAY into the future with issues 48-55 - at least it doesn't skip any....
What happened to comics 19-47 ?
Are they not worthy of being included in an 'ultimate' collection ?

The Ultimate Collections were intended to collect only the issues done by Eastman and Laird (either collaboratively, individually, or just as story plotters like during City at War). So any issues they weren't creatively involved with are skipped.

Fans have to explain this so much, I wish they put a note in the collections themselves!

Ok, makes sense - is there such a thing as a complete collectionof ALL the comics, regardless of who drew or wrote them ?

Unfortunately, no. The recent Mirage Compendium series promises to include all the issues that are narrative canon, though volume 1 already excluded TMNT issue 8 (it might be included in a later volume). There's also the problem of rights issues with some of the guest stories, like everything by Rick Veitch; not every issue of the Mirage series can legally be reprinted without a royalty system set up (that Viacom won't pay).

Mirage is one of those series with such a complicated publication history, we'll never get reprints of *everything*, unfortunately.

Most of the other Vol. 1 issues were reprinted in the classics collection trades.

Yep, vol 2 of the compendium as announced will exclude issues 24-26 and 30 as predicted. Always a shame with the Veitch issues. And then 41 will surely be excluded if they continue the series.

All that is to be expected, and at least the compendium includes 13, and some of the b&w versions of issues that haven't been printed in decades. But it was a shame the timing of compendium 1 worked out so poorly with the issue 8 kickstarter. It's frustrating to take another step backwards from completion, though it's good they respected the rights situation.