When I started brewing I would brew a batch, put it in the fermenter, and buy a case of pop top beer. Drink for 4 weeks, and then have another case of bottles ready to go. Now I have a mixture of tall neck and short neck bottles. If I were starting out from scratch, I'd restrict my purchases to tall neck only for the following reasons:
1. Tall neck bottles won't fit in a short neck cases.
2. Short neck bottles tend to gush more on brews that get over carbed for a variety of reasons.
3. Short neck bottles are a bit wider in the base than tall neck. I can fit 3 short neck bottles in a tall neck rack but not 6.
4. Most craft breweries seem to prefer long neck bottles.
I also like the look of short neck bottles. If you must use them, use only them for the reasons described above.