I too started with the skill tree option, and I like it although it made the game very slow going for awhile there. I seem to have gotten a bad roll, because all the nearby towns seem to only have wood, stone, or copper gear. It looks like some of the faction towns out there may have advanced gear (they are wearing some nice stuff) but I'm going to have to do alot of mining to build up my faction score with them. Once I'm a friendly I hope I get access to their store or else I'm going to really be ticked off. Because currently it looks like that's the only thing that you might get out of becoming friendly with a faction, right?
EDIT: I apologize for my previous response, which had some errors. I was basing on the "official" servers that I had been on. Apparently there are game modes where you literally start with nothing, which is fine if you are expecting it... working for it is fun too. I agree that some of the basic lighting scripts should be available in towns (lvl 2 or 3), if they haven't been added already. Most furniture can be purchased at level 2, but scripts you still have to discover in hard core mode for most important items. I was surprised that the wooden bow was only available for purchase in a level 3 town, instead of level 1 or 2. Other than that the flow of items in shops was pretty good. By the time I found a wooden bow (for purchase), I was already using a steel bow. LoL. Also, the scripts are not updated automatically in all servers... only on the "official" servers. This may be a bug, but most of the time I did not have to purchase scripts that were available: they were added to the replicator as soon as I visited the shop that sold them. On the player servers you have to find or buy and learn everything.
For "Official" servers -- the ones that I have played on:
Most of these "basic items" are (now) included in Adventure mode at startup. Advanced gear is available from towns farther away from the start point (which is usually close to one of the corners) so expect the best gear to be found in towns near the opposite corner. Many scripts are updated (added) automatically when you visit the shops, so check your list again before buying scripts from the shops. The highest level scripts can only be found in high level dungeons, but the gear can be purchased in shops if you don't have the scripts. Also, nearly all necessary resources except Titanium and Lithium can be processed (acquired) in your Colony Processor, so minimal mining is necessary once you build your Colony, and those resources are inexhaustible as far as I can tell. I only mine the Titanium and Lithium after I have maxed out mining skill and equipment (energy tools and max resources) so that nothing is wasted... but that's just me.