John,
Things are not as bad as they seem, based on your reply.
(1) There might have been some submissions based on these, but obviously they have not been picked up. It could be that they were not specific enough, there was not enough information, or they did not make the cut on priorities. Making clear submissions - one for each issue - should help resolve or 'promote' these issues.
(3) You can get the GO statements without too much trouble. On the Generate Package DDL, take a look at the Use [ ] as SQL Terminator entry. Instead of the default ";" enter GO instead, and make sure that you clear the checkbox for on the same line (I think it is cleared by default). This will issue a GO statement after each statement, but that's probably acceptable in the real world. An alternative is to create separate SQL file for each set of entities - tables, views, and such - and string them together with a hand-built file (which you could generate as a stored procedure). Not good.
(2) I think you're in luck, at least to some extent. EA does allow you to model stored procedures, again to some extent. If you are creating your own procedures you can define the parameters. Regardless of whether calling stock procedures or writing your own, you've got to write some code. EA will import procedures, but it is fairly limited in reverse engineering them. Read the documentation carefully, and play around with them a bit.
Note that EA has two methods for creating stored procedures: as single elements, one for each procedure; or as a group of procedures in one element (you can have several of these, grouped by any criteria you choose). However, on reverse engineering, EA seems only to use the single procedure per element mode.
Coda: (3) We keep asking for direct access to the DDL engine, but thus far no go. Yet another suggestion that needs to be made, repeatedly. But...
HTH, David