Thanks for the feedback. Items 1, 2, 3, and 8a are already feature requests and I have added your comments to our existing tickets. I have added new tickets for the remaining items. I know you already know the work around for these most of these items but I will comment for those who do not.
1-2) specific spacing for individual holes. First place a small hole on your layout and assign it to phantom net (a net that will not be used on your board except to adjust spacing for a specific hole size) and adjust the net spacing to accommodate the clearance you want. You can then place this hole inside the original hole to adjust the spacing. This will result in a DRC warning but will result in the desired outcome.
3) We are currently adding slots and cutouts to PCB123 and this feature will be available in V5. Until then the following link explains slots and cutouts in PCB123. Creating Slots or Cutouts
4) This is a major enhancement. No work around available for this functionality. We are aware of the limitations of copy and paste and will work to improve this with future releases.
5) As stated use wide traces to increase thermal width.
6) Similar to the solution for items 1-2 you can use a plated hole over the existing hole to control solder mask relief with some limitations for very small vias. The minimum via size is smaller that the minimum plated hole.
7) Copper regions can be unmasked by including a filled polygon on the solder mask layer in the size and shape of the desired solder mask opening.
8b) You cannot add traces in the footprint edit but you can add polygon lines which can be used to connect pins in the footprint editor. Once you use a polygon as part of a footprint you lose the ability to assign the polygon to a net which will result in a drc warning when you place the footprint on your layout, but this will provide the desired connection.
Please feel free to contact customer support if you have any questions.