I think there both underestimated pins (especially the Doctor Who, which is currently 16th on the "Bang for your Buck" list for a reason) and they both offer great price / fun value.

However, Flintstones is imho a bit more for the average player, while Doctor Who is more difficult (to initially understand and to play) and a machine that advanced players tend to appreciate. This also goes for the theme I guess, Flintstones being more kids friendly and all.

Both machines are focused around multiball, but in Doctor Who this is a more difficult task as you have limited time to get it (get the 4x playfield score and then go for the multiball as fast as possible, frequently ending up draining your ball because of the time stress).

I love the high pitched screaming and the Sonic Boom sound from the Doctor Who pin, however be warned that your neighbors might not. And I agree that the bowling part is a lot of fun in the Flintstones pin.

Bottom line, imho Flint Stones is the more accessible of the two (both in appearance and in gameplay), but Doctor Who has more challenging gameplay and thus probably better lastibility.