In a close election, allocating the EVs proportionally by vote within each state actually tends to tilt things slightly towards the Republicans (relative to their showing in the popular vote), since they tend to do a bit better in smaller states, which have a bigger proportional bonus in the EC with the +2 EVs for senators.
For example, I think if you allocated the 2000 EVs by popular vote in each state, then Bush wins the electoral college more decisively (without the need for a recount), despite losing the popular vote nationwide.
Wrong. While you're right Bush would get more EVs, he only gets a plurality. By one. And it's thrown to the House:
G B N
AL 4 5
AK 1 2
AZ 4 4
AR 3 3
CA 29 23 2
CO 3 4 1
CT 5 3
DE 2 1
DC 3
FL 12 12 1
GA 6 7
HI 2 2
ID 1 3
IL 12 9 1
IN 5 7
IA 4 3
KS 2 4
KY 3 5
LA 4 5
ME 2 2
MD 6 4
MA 7 4 1
MI 9 8 1
MN 5 5
MS 3 4
MO 5 6
MT 1 2
NE 2 3
NV 2 2
NH 2 2
NJ 8 6 1
NM 3 2
NY 20 12 1
NC 6 8
ND 1 2
OH 10 10 1
OK 3 5
OR 3 3 1
PA 12 11
RI 3 1
SC 3 5
SD 1 2
TN 5 6
TX 12 19 1
UT 1 4
VT 2 1
VA 6 7
WA 6 5
WV 2 3
WI 5 5 1
WY 1 2
262 263 13
48.7 48.9 2.4