Pandora thread has been hijacked to the point of no return so I might as well chime in. BU and proof coins have separate supply and demand profiles as Pandora mentioned. Here are some recent transactions to get the discussion going:

1990 1/2 MS69 SD sells for $2200 (NGC 90) while 1990 1/2 PF69 sells for $1300 (NGC 163) - makes sense

1991 1/2 MS69 sells for $1600 (NGC 266) while 1991 1/2 PF69 sells for $1700 (NGC 133) - proof appears to be undervalued

1992 1/2 MS69 sells for $1250 (NGC 246) while 1992 1/2 PF69 sells for $3000 (NGC 64) - makes sense

1993 1/2 MS69 sells for $1500 (NGC 274) while 1993 1/2 PF69 sells for $1250 (NGC 131) - proof appears to be undervalued

1994 1/2 MS69 sells for $6500 (NGC 301) while 1994 1/2 PF69 sells for $5500 (NGC 86)- proof appears to be undervalued

Many proof don't fit into master set demand at this moment and so they look cheap relative to their rarity, if future master sets include proofs or a dedicated set with only proof coins is demanded then prices will adjust upwards for the proofs, if proof master set doesn't emerge then eventually the proofs will be more common relative to BU because all the BU coins are stuck in master set. Nobody can predict the future but one can make the future simply buy accumulating enough proof coins and then marketing a master set.

I cover my bases and accumulate both coins, not trying to outsmart the market when supply for both is so limited right now.