The common reason given as to why there is no Talmud Bavli on most of Seder Zeraim or Seder Taharot (only the tractates of Berachot and Niddah are represented) is that the Amoraim were based in Bavel (Babylonia) and lived after the time of the destruction of the Temple. Therefore, the laws pertaining to the agriculture and land of Israel (Zeraim) did not apply, and neither did the laws of ritual purity (Taharot). Yet almost all of Kodashim has Talmud Bavli on it; the Amoraim clearly discussed Zevachim, Menachot, etc. even though there was no Temple. Now I am aware of the verse that says "U'Nshalma Parim S'fateinu," indicating a special concept of reward for discussing and studying sacrifices, even when they can't be brought (i.e. since there is no longer a Temple). However, we also are rewarded for studying laws that no longer apply like Zeraim and Taharot, so why did the Amoraim not discuss them the way they did Kodashim?
The simplest reason is that the main topic matters of Zeraim and Taharot are only pertinent to those who live in the land of Israel. Zeraim (apart from Berachot, which is included in the Bavli) deals with agricultural laws, all of which are primarily relevant for those residing in Israel. Taharot (aside from Niddah, which is included in the Bavli) also only really mattered in Israel, especially when the Beit haMikdash (temple) was still standing. Thus, (as Joe points out), the bulk of Zeraim and Taharot were not taught as units in Bavel (as opposed to the academies in Israel, the discussions of which became the source material for the Talmud Yerushalmi).
It is worth noting that mishnayot and beraytot from Zeraim and Taharot are quoted throughout the Talmud Bavli, whenever they are needed as related material for discussions germane to the topic at hand.
I think the answer to this lies in the Talmud's origins. It presents itself as a series of discussions, but it wasn't as if Abaye and Rava were having an argument while someone took notes. What really happened was that the positions of the Tannaim and Amaraim were incorporated within lectures given in Babylonian yeshivot and programs like yarchei kallah. These lectures followed the Mishna, but they didn't necessarily cover all the Mishna - just like today, different programs or academies would have a study cycle that covered different bits of it. The source material was transmitted and refined over literally hundreds of years until it became a huge, dense corpus of discussions that was the basis for the Talmud. It was eventually redacted (by the Savaraim) and that's the Talmud we have today.
So why is there no Talmud on most of Taharot? Well, recall the Talmud's origins - it documented the course of study in the Babylonian academies. If there were no courses on a chapter of the Mishna there would be nothing to be redacted, and if there only a few courses the material may have been too brief to justify its own tractate and been included elsewhere.
I realise that this answer just pushes the question back a step - why were there courses on most of Kodshim and not on Parah? I suspect it was a snowball effect that started because there was initially more demand for courses on particular tractates. This created a corpus of material on the tractates that had been studied, which justified further courses and eventually led to this material being redacted in separate tractates.
Incidentally, this very likely explains the mesechtot ketanot like Sofrim and Semachot: they contain material that was treated separately by only some yeshivot, so you end up with specialised tractates even though a lot of the discussion is included elsewhere in the Talmud. So from the fact that there is no masechta Parah we can surmises that there was no regular course of study on it. On the other hand, there was so much material on Nezikin that it had to be split into three courses (First Gate, Second Gate, Third Gate).