Advantages of using Newer DS as a base.

1- it has some ASM codes that were not used much by Newer Team and you can take full advantage of them.
2- better stability and performance since it has a little more internal RAM.
3- some improvements with respect to "NSMB"
4- you can add more ASM codes.
5- less development time.

Disadvantages of using Newer DS as a base.

1- some levels are complicated to edit since they use areas from other levels.
2-some sprite functions crash the game for example the buzzy beetle "Upside-down shell"
3-some sprites have complicated functions.
4-some tilesets have animations but their animation files are well hidden for example "Starry Space"
5-same as disadvantage 4 the BG's have well hidden files for example "Space Fall"
6-level maps are complicated to change (unless you have the knowledge to change them)
7-music is difficult to change since it has a soundfont set for it to work correctly

Now the advantages and disadvantages of using NSMB.

Advantages of using NSMB as a base.

1-you have a blank canvas to work on a mod from scratch
2-you can install ASM codes either with the traditional engine or with NCPatcher
3-you can change level maps easier
4-levels are easier to edit.
5-All tilesets and backgrounds are easy to modify or change.
6-All sprites work correctly.
7-Music is easy to modify or change.

Disadvantages of using NSMB as a base.

1-You have to install ASM codes from scratch and if you don't like the ASM code and you have a great advance in your mod, then there is no way to start over in a new ROM. (of course unless you make backup copies of your mod)
2-If you put a lot of sprites the game slows down. (Compared to Newer DS which can support more sprites I think XD)
3-Some graphics are complicated to edit like the logo and world icons. (Unless you use ASM codes)
4-Add files that require ASM codes. (Unless you have knowledge in that)
5-Modify the "Overlay" files because if you make a mistake the game can crash. (unless you have knowledge in that)
6-more development time.