You can definitely merge the units together either way by buying both games… as previously mentioned, 1942SE has more unit types than 1941 (specifically Artillery, AAA and Cruisers), but for the most part, everything is self-complimentary in boosting the overall pool of available units.
Also, the 1941 and 1942 versions have different sculpts for each unit (aside from the infantry which is identical). The 1941 version has a different tank, fighter, bomber, destroyer, carrier and battleship sculpt/model (1-each) for the Axis and Allies respectively (things such as a Tiger Tank, He-111 bomber, FW-190 fighter, Hood BB, JS-2 tank, Russian carrier, etc, etc). This is a plus, not a minus, and a nice way of adding cool new looks to both 1941 and 1942 (since the 1942 sculpts are different than the 1941 sculpts and vice-versa).
I got back into A&A by purchasing 1941, quickly followed by a purchase of 1942, then pooling all the units together in common bins for use in either game. I also boosted that further by purchasing more units from HBG to make it possible for me to play a “chitless” game if I so choose in either version (assisted by printing larger maps to give more room, but that’s another subject). For example, all five of my powers have over 60 infantry and 24 tanks in their bins for each nation. I highly recommend doing what you asked… just buy 1942 and merge them… if you want more than that, go on HBG and order additional units.
Enjoy the game, its a lot of fun.