1. e3 !?

Possibly influential:

https://www.qualitychess.co.uk/ebooks/e3_Poison-extract.pdf

I have no idea where you got the conclusion that 1.e3 is passive.

It will most likely lead to either English or Reti and neither of the 2 is passive.

   The only problem with 1.e3 is that it is hard to play it reasonably without transposing to something else.

   After 1...e5 2.d4 transposes to French exchange after 2...exd4 3.exd4 d5 ,2.c4 is English ,2.b3 is Nimzo Larsen and these 3 are pretty much all the reasonable options.

    Maybe 2.Nf3 and an attempt to play Alekhine's defense with colors reversed is also reasonable(Bent Larsen has done this but with 1.g3 first move instead of 1.e3) but again if Black responds 2...Nc6 White's only choice is to transpose.

    Pretty much that's the reason 1.e3 is not played in high level. The same is the case with the other 2 rare moves, 1.Nc3 and 1.d3 .Nothing wrong with them but difficult to find indipendent value unless you are willing to play unreasonable moves.

1.Nc3 will transpose to something else as well.

What will you do after 1...d5?

2.e4 transposes to Scandinavian, 2.d4 transposes to Richter Veresov , 2.g3 transposes to Benko or Reti(if Nf3 follows) with the usefulness of the early Nc3 rather doubtful ,2.Nf3 delays the possible transpositions but after 2...Nf6 White is out of reasonable non-transpotional options.

     There are many other lines. What do you do after 1.Nc3 Nf6 if Black wants to play a King's Indian defense? What else except transposing to Pirc or Reti?

     What do you do after 1.Nc3 c5 if Black follows again with Nf6-g6-Bg7? It's either a d3 and e4(with or without k-side fiancheto) or an e3 and d4. What else? And you can't dealy the decision for ever , you don't have unlimited waiting moves. After 1.Nc3 c5 2.Nf3 Nf6 you have to decide and all decisions transpose to something else that does the same job better.Unless you play unreasonably  which is pretty much the only way to avoid transpositions. 

       1.Nc3 is a perfectly fine move , I tried to make it work without transposing when I was a kid but I realised it's not possible. It's not a coincidence that very few and very rarely play 1.Nc3 and none has it as his main move while many play 1.Nf3 and a lot have it as their main move.

    Here is a game played in chess.com league and as you can see Mamedyarov doesn't find a way to avoid the transposition to Richter Veresov.

Those who play 1.Nc3 regularly also haven't found a way for white to avoid transpositions.

 you never heard of the book "knight on the left"? its a well known book, and its the bible of 1.nc3  i find it strange that you consider 1.nc3 d5 2.e4 to be a line of the scandinavian. its the van geet attack, and its always been known that way.

1.nc3 c5 and white can choose between 2.nf3 intending an early d4 WITHOUT an early e4,or even 2.d4!?

white can also play for original lines if white insists on caro kahs and frenchs. for example 1.nc3 d5 2.e4 c6 3.qf3!? or 1.nc3 d5 2.e4 e6 3.g3 intending nf6 4.e5 nfd7 5.f4

1.nc3 nf6 is best to transpose to something like veserov or jobava attack, or vienna gambit or 3.g3 vienna, but even moves like 2.g3 or 2.f4 are possible.

you need to think more creatively. regardless, so long as white doesnt absolutely insist on no transpositions (1.nc3 nf6 being the most clear exception , he can usually play independent lines at leisure

If you like the ruy lopez with Black you could try 1.e3 e5 2. e4!

Interestingly, 1. e3 is the third most played move on chess.com according to the Game Explorer: http://www.chess.com/explorer/index.html?db=2

Since when did e3 become popular?  I suppose one could play a reverse French Defense (1. e3 e5 2. a3 d5 3. d4) or a game could transpose into a queen's pawn opening with 1. e3 d5 2. d4.  Can anyone shed some light on this?