Well, this is just my opinion of course. Also, you may now know this already but I will say it anyway.
You probably do not want to start out with the 10 level ship. The caveat is that if your energy and weapons are not level10 you will continually get blown away. I believe you will then be fighting enemy that are level 10 - correct me if I am wrong.
The mesa mod is good if you know how to use it. Basically, what it does is it allows you to upgrade you ship faster by needing fewer crystals for each upgrade. For instance, as you normally progress you will need, example, 4 crystals to upgrade, then later after several upgrades you will need 7 or maybe 10 to get to the next level. The mesa mod changes that so you only need 3 or 4 crystals far into the game allowing your ship to acquire crystals faster, hence new ship upgrades faster. This actually works really well and doesn't seriously take the enjoyment out of the play.
As you upgrade you will be traveling to new systems and in these systems the various higher equipment, weaps, engine, and energy upgrades will be available to you. If you start out with a level 10 ship in its basic configuration your chances continuing on are going to be really hard to do. (Mainly because at that point in the game you can not get the higher level weapons you need and your shielding will be inadequate.) Example, your level 10 ship with level 1 weapons and hardly any shielding will cause you to die from the enemy level 10 ships with level 10 weapons and related shields. I read somewhere where there is a slight twist to this involving what about your level 10 ship actually causes the enemy to be level 10, but I can't remember what that was right now.
Simply put, start the mesa mod if you want, then play the game normally. ONLY upgrade your ship as you receive the crystals. All will be well then, but your ship will become much more powerful faster then with no mesa mod. This method does work much better then the default upgrade path. The biggest issue I had with Pirates is their relentless swarms. I developed tricks to deal with that, like during the start of the game, when I went to take out a pirate system, I would make a run to the nearest space station and use it's shields that would allow me to last long enough to take out the waves of pirates. If I did get blown away and not make to the space station fast enough I would just restart the level as each time the pirate attack scenario has changed enough to make a difference.