I don't understand the question. If you get indexed with site A it effects any future indexed neither negative nor positively unless you link to the new sites..
If I understand your question...I think because of the so called "trust factor" with G I should think that it would make most sense to have your site indexed from a trusted source...where might the BEST source be...well maybe dmoz or the yahoo directory...but let's get real that ain't gonna happen overnight. So I'd say submitting your site slowly to some trusted higher PR general directories would be a good way to get found OR even a link on a similar theme'd site. It seems that today sites that are getting found with "gray hat" methods such as tag & ping or mass recip link trades aren't seeing the reward with good rankings they once saw a few months to a year ago. Again this is just my 2 cents...
Paid directory links are alot of times not anymore valuable than the free ones unless of course the whole directory is paid and it costs over $20.
No, as long as its a good site. For example: If I have a choice of getting indexed by a PR4 site and a PR3 site I wouldn't care too much as long as it gets me indxed. I would probably choose PR4 but thats not the point. As long as they site is valid and legit than it doesnt matter what specific sites to get indexed from, although good PR and SEO'ed sites are always better.
who cares who indexed the site first. Good thing is to get indexed. And the big 3 are good to index. Thanks