About the recommendations, id say no to a thaumcraft NEI plugin. Simply because itd remove the need for the thaumiconicon which personally I like, feels more indepth searching around it for different things and like I'm using the mod to its full and intended potential.
thats still up to you. i use both. it is client side.
and trust me, it wont replace the book with all its descriptions, manuals and research notes.
but like me, if you read the book like a thousend times and almost know every recipe from the top of the head, the book becomes a pain with the scrolling/dragging around/skipping pages with descriptions and stuff without a bookmark... and dont get me started on the mouseover-list of items that have a certain aspect.
this infact is the main reason for me to use the plugin with its the ability to look up aspectitems in a very tidy interface with pages.
I personally think it has potential to be enabled on default. There are a fair few issues with it by the sounds of it but if the mod dev is active and willing to add (forgot what it's called. My minds gone blank) support for the recipe changing thingy so we can alter stuff, then it could add another level of complexity and awesome ness.
Everything else in minecraft is based on ores, processing or magic. This is the first mod ive seen to fully bring in protons, electrons and similar things. I'd love to learn more and get into it to see what crazy stuff I can make.
Edit: MineTweaker! That's the one!
right now it randomly makes the launcher to get stuck in a loop (at least every second time).
even though it got potential, this is a functional problem.
especially newbies will abadon a modpack that is 'broken' without a second thought.