It takes a smidgen of effort to make Linkman more Powermarks like, and then you have to push yourself a bit, however it is worth it. You will find that the advantages will balance any disadvantages and that you are moving forward, especially in having new features as the latest updates show. Now to your 3 concerns.
1. No Automatic Suggestions while entering Tags. Here PowerMarks always used to suggest previously entered Tags, as one typed.
Not sure how that works for you. I always pick up the metadata anyway, with both programs, and then add keywords particular to the moment. Rarely do I add exactly the same as the previous entry so there may be a Powermarks feature I never used. On the cases when I do want to dup the previous entry I use the clipboard. (Usually that is in the name fields for alphabetizing, since I use Linkman as a PIM, as I did Powermarks, in the future I plan to do similar alphabetizing-sorting with the user-defined fields that are Linkman-specific as well.)
Note: They have been enhancing the printing as well, which is a very big plus over Powermarks, where my print function was usually the screen capture program. In this function alphabetizing is helpful, since the sorts match the query sorts (new feature).
2. Folder structure.
Here your comparison is not with Powermarks but with a program I will have to look at, so I will pass on commenting much. The ability to have a folder structure in Linkman may have some advantages, and perhaps that can be changed structurally as you suggest for pizazz. However the Powermarks "no-folder-at-all" structure can be reasonably emulated in Linkman, the key issue in comparison. We can't fault Linkman for both having folders and letting us hide and unuse the folders ! Especially if we are trying to enhance the folder concepts.
3. Duplicate deletion
Your points about dups are well-taken. However Linkman just made the major enhancement on this, which I discuss above. They still don't radically prevent dups on the data-manipulation level, (they can still be made in imports, their deliberate design decision, understandable yet worthy of more discussion) however they definitely now properly move you into edit mode when you go to "add" (update) an existing URL, as long as you have the no dups configuration option checked. This was the major Linkman lack, now fixed. The only awkwardness is that they did not "Replace" the word "Replace" with "Edit" or "Update"
-- however once you understand how it works, that is more cosmetically semantical than a problem. Oh, yeah, Linkman may have one more click involved. We can ask them to make eliminating that click a configuration option "Always bring up existing URL" as a sub-configuration under the no-dups checkmark.
The big difference I see is that I frequently had to dup-text (cut-and-paste) on Powermarks the name line to see the entry, the same words in the keyword-tag section. To be sure it showed up in search. With Linkman you can specify that the name field is part of the keyword search anyway, no dup necessary. Now granted I was using the "Keyword Search" on Powermarks, not the "Exact String Search" and Linkman just added the "word search" function as a default configuration option, so I may have to check this a bit if the goal is accurate comparison. Linkman is more flexible with wildcard-style characters and boolean, how much this is used will vary a lot.
Why would anyone deliberately want to allow dups ? Well, you would have to ask around. If you want to use Linkman as a PIM, I can give an example. While in googlebooks every page can easily be a new link, this is not the case on archive.org. So if you wanted to make a bunch of easily-read notes (in the name field) for a book, ("p. 20 about Messianic expectations, p. 75 about the Johannnine Comma") you could have the same link 5 times. Not the most elegant, and I don't do that, but one possibility. There are probably others. I agree with the no-dup philosophy for me personally, however Linkman may have a number of customers who like the dup-option.
It might be good to list the 5 or more significant advantages, and the differences between, Powermarks and Linkman. It is no knock on Powermarks that Linkman is able to be competitive, Powermarks has been truly fantastic for years. If the fellow from Kaylon had kept at it it would have been neat. He never really gave us much visibility and moved in other directions.
Understand I am no slouch when it comes to using programs others consider dated. Eudora is my email of choice, and I have looked at Thunderbird, the Bat! and the kitchen sink. If it wasn't for Linkman I would be using Powermarks and would have tried hard to have gotten those AutoHotkey kludges working !