Think of e-Organizer as your conventional organizer in an electronic format.  The advantage is that your client's data entry can be bridged into Lacerte once you get the file back so that you don't have to spend time repeating those same keystrokes.  The downside is that you should spend time reviewing your client's input before the import so that you don't have to play Where's Wally when you start to review the return (hint: avoid garbage in, garbage out).

Think of Intuit Link as a client portal.  The questionnaire and document checklists, although could be customized by proforma in a limited sense, are very generic and rudimentary.  If you rely on those, you should expect to have a lot of back and forth with your clients, following up for and clarifying a lot of the details you need - unless, of course, your clients' are run of the mill returns with only W-2's and basic 1099-INT/DIVs.  Documents such as 1099-INT/DIV, W-2, K-1 can also be imported into Lacerte.

I've only used Intuit Link, and I agree with you that there was a lot of back and forth with a particular client, and the client was not happy with the extra time spent/billed.  We went back to paper organizers for them the next year.  

Out of hundreds I only use it for one out-of-town client.  We have our own portal now, so not much benefit using Intuit Link with the extra hassle.