I use El Nikkors, Rodenstocks, and Schneiders. I see little difference in overall quality from one brand to another. I'm not sure that making the change you suggest would be an "upgrade" unless, perhaps, you're considering an APO enlarging lens.
I don't think it's worth upgrading the EL Nikkor to a Rodagon or Componon-S, but it may be worth upgrading to an Apo-Rodagon or Apo-Componon.
Since they've come down in price so drastically, I've upgraded to all Apo enlarging lenses. They're sharper at wider apertures and typically have better contrast than standard lenses. I use 50/2.8 and 90/4.0 Apo-Rodagons and a 150/4.0 Apo-Componon. I could see the difference even with small prints when I compared them with the lenses I was using (6-element Rodagon and Componon-S and one 4-element EL Nikkor).
I don't own any APO enlarging lenses (maybe someday!); my comment was based only on my reading. I understand that APO lenses may offer some slight improvement, especially at larger apertures (see David's comment above).
I have no experience with either EL-Nikkors or Rodenstock enlarging lenses, but I went from a Schneider 50mm/f4 Componon to a 40mm 2.8 APO Componon HM, and it was like trading a Holga for a Hassy - knock your socks off difference, even just printing B&W.
[COLOR=SlateGray]"You can't depend on your eyes if your imagination is out of focus." -Mark Twain[/COLOR]
By strange coincidence - I just happened to spend Saturday doing some 50mm enlarger lens testing, and I wrote it up as an article yesturday!!!! I'm just waiting for Sean to adjust my upload limit, so I can upload the whole article as a single pdf.
The results aren't particularly thorough, but they are surprising. I did some prints with an El-Nikkor 2.8, a Schneider, and a Minolta. I suspect there was some experimental error, so will do more testing in the future - however the results are dramatic.
Without giving the game away, I may not be using the Nikon too much in the future (but then I might not be using the schneider either!).
Oh well, that's maybe good. I moved and I seem to have lost my box of Nikon enlarger lenses in the process. So I got me cheapo 50mm Rokkor 2.8. I got it cause it was on a lensboard and I figure, the price is worth the lensboard alone. I mostly print 6x6 negs anyway so i got a Componon-S 80mm. I wonder if I'll notice the Holga prints from my Nikkor 80mm and my new (used) Componon-S?