I do not have a single edition to recommend, but here are some things to look for when choosing a Shas.
My credentials: I use a huge 35-year old "yellow" Greenwald edition of
the Shas daily in my Daf Yomi shiur, a tiny Oz Vehadar to prepare on
the bus (5 days a week) and whatever is available in the various shuls
that I learn in.
Pesukim - Verses
The advantage of the "old" layout is the ability to see at a glance where a verse came from. The narrow margin around the gemara had that information.
In the newer versions you have to follow a tiny letter (usually one of 3 or 4 in different fonts) to some random location on the page. This location usually changes from page to page, making it difficult to "glance" at a reference.
The advantage of the newer layout is that you get to see the entire verse; having it in context often helps one understand the Gemara. Sometimes the portion of the verse being discussed is actually missing from the actual text of the Gemara.
So ideally you'd want to find a version that has inline references (in the tiny margin between the Gemara and Rashi/Tos.) as well as the full Pasuk. IIRC there used to be a "red" version that had this.
You want to ensure that each "marginal section" has a distinct "referring" font, otherwise you'll become frustrated deciphering which section to go to for which letter. Some version even use digits for the Pesukim, making it distinct, hence easier.
Cross references
In the older layouts you can see at a glance to the margin where the related Gemarot are. Knowing where the issue is discussed elsewhere often provides a clue to the context.
In the newer layouts this is also hidden behind a letter referencing a random spot on the page.
Alternate Girsaot and tiny remarks
In the older versions the margin is splattered with alternate versions of the text as well as some comments.
In the newer ones they are also hidden behind a letter, often making one unaware of their existence. Some of the newer version have at least highlighted the word(s) that matters, in the random spot on the margin.
Commentators at the back
Some of the newer versions have taken the dozens of Meforshim at the back of each Masechta, and made them into a compendium. This saves a lot of time.
However, some of the Meforshim have disappeared; potentially being lost "forever".
Also, some of the newer versions have not redone (all) the the meforshim at the back - and some of them will still be hard to read.
Rashi's French
Some - but not all - of the newer version have a translation of Rashi's foreign words on the page. This is very useful.
Rashi elsewhere
Some of the never versions have added to the page Rashi's comments elsewhere on related topics. This can be very useful. Others have out this at the back, leaving more room on the page.
Margins
The older layout has a lot of room in the margin to add your own notes. In some of the newer version, every spare millimeter is occupied.
עין משפט השלם
Many years ago there was the "red" set that printed the full version of the referenced Rambams on the page.
Some versions may have this in the back, nowadays.
Tiny letters
Make sure all the tiny letters are readable. Some printers have fonts that are easier to read than others. Also check the last few volumes; many of the Kodshim volumes have smaller fonts in the original Vilna Shas, (more words on each page) and the newer editions may have trouble with that.
E&OE
Keep in mind that newer version can also potentially introduce new errors. I have found that the new Mishnayot (Zecher Hannoch) and the new Chumashim have their own collection of typos they introduced.
All the meforshim
30 years ago they started printing huge volumes where each Masechta included "all" the Rishonim and popular Achronim.
At the time we were learning Bava Basra with the Rosh Yeshiva, Rav Shlomo Zalman Auerbach זצ"ל. When he noticed this new Gemara his comment - said in jest - was: "Wasn't Bava Basra big enough?".
