I had to use two different maps in order to show you more details, but the numbers on the places are matching, so you can check for more angles of the same parts of map..
1- No Greasy Joe's, instead there is flat land and a tall billboard
2- No big apartment near Callahan Bridge, its just a flat grass land
And here is another beta map that shows the beta version of that building, it seems to be completely different and it kept a big part of that land too. Unlike the final version covered the whole land and had walls surrounding it.
3- There are two warehouses near LC Sawmills instead of only one, and they are faced to another way. Also LC Sawmills too seems to be placed slightly different than the final version.
4- In the final version, the warehouses seems to be placed wrong, as the cement land before them is in wrong position, in the beta, the warehouses placed slightly different, but in their correct positions.
5- Portland had an extention of land, appears to be industrial, not state penititiary
6- There is another warehouse behind Bolt Burgers building, according to another beta map
7- There was a beta factory in the place of Burke Supply Company, and with removing of this building caused Burke Supply Company to be moved in its place, thus explains why warehouses in the wrong places. Because they had to cover up the emptiness that Burke Supply Company left behind it.
A pic from final version of map (via Moo Mapper)
8- Liberty Pharmetucals had only one big chimney instead of 2 slim ones in the final. Also there was a water tank in its roof too.
9- Same goes with Joey's Garage, it had only one big garage door instead of 2 slim ones in the final.
10- AmCo HQ was facing to Joey's Garage instead of Liberty Pharmetucals, and had another warehouse near it.
11- Docks didnt had any walls surrounding it, also there was a road going in to that area.
12- There was extra stuff behind Liberty Pharmetucals instead of empty cement area.
13- There appears to be 3 more warehouse near Head Radio
14- The tall building behind bolt burgers seems to be absent
15- There was no Supa Save, as the tunnel entrance can be seen easily
16- Original bitching dog factory seems the be really different.
17- SemTech Building appears to be much shorter than the final one.
18- Wang Cars was to be featured in GTA3, but it seems the idea was scrapped and it's sign re-used for Greasy Joe's in the final version
And here is the LOD of Greasy Joey's sign, that proves it was originally belonged to Wang Cars
19- There was more telegraph poles around portland
Borgnine Taxis didnt exist until the latest stages of the final version of the game, as the lod and overview ipls proves that it was only an grass patch. Also i removed borgnine taxi's building from that area and he grass patch still exist in the same way, the collision of it also works in the final game too.
Luigi's Club had a Cheetah parked in front of it, possibly belonged to Luigi himself. I checked it numerous times and its doesnt belong to the traffic (npc) its just parked in front of it.
Import export garage looked different in the beta version, and the unused import export garage ended up using by atlantic quays area:
It seems that Columbian Cartel Mansion also werent present in the beta, just looking through lod of that map clearly states there was a grass patch just like borgnine taxis situation.
Same thing happens to Staunton Fire Station aswell
Joey didnt had his tuxedo in beta, in fact, he was wearing his work clothes (this error still exist in some of PS2 versions of the game, but fixed in XBOX and PC)
Some new pictures proving that there was more telegraph poles around Portland
XXX Magz looked different and also had a different logo
Luigi's Club looked way different back then
Panettiere (Used in bank robbery mission)
This road added way later in to the game
LC University changes