The whole business of MCPD variations and upgrade exams has proved to be a confusing area. Vishal Joshi wrote a post back in April on dynamics of the upgrade exams, which is very helpful.
I have tried to put this into a graphical format. The following diagram illustrates the requirements for MCTS/MCPD certifications. (I hope I am not making it even more complex!)
Top section of the table shows the competencies earned by passing each exam. Bottom section shows which competencies are required to earn a credential (certification).

If this table is clear enough then you can ignore the rest of this post. Otherwise, read on!
What is a "Competency"? Knowledge and skill in a particular area. Normal (non-upgrade) exams test one competency only whereas upgrade exams test two or three competencies. These competencies map to different sections in the exam. For example 553 has three sections so it is testing three competencies.
Please note that "Competency" is not the same as "Certification". New developer certifications require the candidates to show their competency in multiple areas. For example, in order to become an "MCTS:Windows Developer", you need to earn "Application Foundation" and "Windows TS" competencies.
There are a total of seven competencies to be earned in the new developer track. I have assigned a letter to each competency for easier tracking. Competencies ending in "TS" show development skills in an area and those with "Pro" suffix reflect the design/architectural skills required to be recognised as a professional in the respective area.
A Application Foundation
B Windows TS
C Web TS
D Distributed TS
E Windows Pro
F Web Pro
G Enterprise Pro
Each competency can be acquired by passing more than one exam, assuming that you satisfy the MCAD/MCSD.NET requirement (shown in the right column). For example, in order to earn competency C, you can pass either 528, 551 (if you are an MCAD or MCSD.NET) or 553 (if you are an MCSD.NET).
This diagram also clarifies why MCPD:Ent (aka EAD) is not a superset of MCPD:Win and MCPD:Web. MCPD:Ent requires ABCDG, MCPD:Win requires ABE and MCPD:Web requires ACF.
Hope this helps!
Update: Microsoft has finally published a page with more details on the upgrade paths from MCAD/MCSD.NET to MCPD. Nothing new really but it is the official word on a subject that has confused so many people out there. It says if you are an MCSD.NET and pass 70-553 and 70-554, you will earn MCTS:Win, Web, Dist and MCPD: EAD (4 certifications in total). If you want to earn all .NET 2.0 certifications (including MCPD:Win,Web), you will need to pass 70-547 and 70-548 in addition to those mentioned above.
It is also good to know that as an existing MCSD.NET, you can get a 25% discount for taking the upgrade exams by 31 March 2007 (Promotion Code: SQV554).