Thank you, Nicholas, for the good work you have done and for the good work you are now to do.
Having read the spell lists, I am now ready to comment on them. I'm going by the PDF versions, so if there's some variance in the HTML version, not all notes may apply to that version. Minor edits included in case the author decides to do a revision at some point.
Staff of the Magi: Eh? This is the one that puzzles me the most. "Archmage Base List" -- the whole thing about the Archmage was not having fixed base lists, and there are existing magic staff lists, should he want to choose one as one of his base lists. So, the motivation to create this list eludes me. That said, level 8 "Charge Staff", should really have a different name, since it is entirely unlike the Alchemist spell of that name. Perhaps "Energize Staff"? In the last sentence of that spell's description, "durations" should simple be "duration". Better yet, the entire word may be removed as redundant. Level 19, "Life Store", is missing the apostrophe in "caster's" and the second mention of "Life Essence Levels" is missing the capitalization of the second and third words.
Bone Enchantment: This is a nice thematic list, but it also has some spell naming issues. Level 11, "Bone Casting True", and level 75, "Lord Bone Casting"/"Bone Casting True", are the first two spells in question. "True" spells are supposed to be the highest form of that spell, while "Lord" indicates level 20. Therefore, the list entry for the level 75 spell should be changed to match the "Bone Casting True" given in the spell descriptions, while the 11th level spell should be changed to something like "Improved Bone Casting" or "Greater Bone Casting". Next consider the level 14 spell, "Skeletal Visage True". There is a "Lord Skeletal Visage" placed properly at level 20, so the "True" label again is misapplied. I suggest "Terrible Skeletal Visage". The final spell I would comment on is level 18, "Ring of Bones". The description tells us that this spell "Allows caster to enchant a single bone... usually carved and crafted from a single bone". The redundancy here should be removed, but it also suggests that the spell name should actually be "Ring of Bone".
Skeletal Ways: Several spells give their duration in "min/lv" rather than the standard "min/lvl". The last listing, for "Lord Skeleton Army" needs fixing. The Area of Effect for levels 2, 6, 9, 14, 15, 18, 19, 20, and 30, should be listed a "1 target" rather than simply "Target" or "Target(s)", or better still, levels 2, 9, and 18 should have an Area of Effect of "1 Skeleton". The duration listed for level 7, "Skeleton Warrior" is listed as "-", whereas the description clearly states a duration of three rounds. There are persistent failures to capitalize parts of monster type names starting with all the "1 Minor skeleton" mentions from level 3 on, and expanding to include several modifers (e.g. "greater") in the level 13 & 25 descriptions. Although I generally like these skeleton-based lists, the level 11 spell, Skull Bomb, is one I'd likely replace. It just seems more like something a Spider-Man villain would use rather than a fantasy element. That's purely my subjective opinion, of course, but there it is. Level 50, "Skeletal Army" should read "may raise a vast army of Skeletons" rather than "may summon" such an army, since the skeletons are not actually summoned.
Chaos Theory: The Chaotic Interpretation spells are asymmetrical in their effect. Was that intentional? One more percent is added to the open-ended high range than to the open-ended low range. To make them the same, for example, "Chaotic Interpretation I" would give "91-100" as the extended open-ended high range. The scaling on the numbering is also off, in my opinion. Chaotic Interpretation I adds 5 to the open-ended low range, making it 01-10. "Chaotic Interpretation II" adds 15 to the open-ended low range, making it 01-20. I would call that "Chaotic Interpretation III" and likewise change the other spell names in this series to keep the numbering consistent with the size of the first step. "Random Perceptions" is described as causing synesthesia. I would rename as such, as more a more interesting spell name. Level 5, "Chaotic Null", and especially level 30, "Accentuated Chaotic Null", seem counter-thematic to me.
Lake Ways: This spell is the one most likely to be of use to me, as it would convert with minor modification to be a RMSS/FRP Priest list. The terms "radius" and "diameter" are used, but unless your lakes are all circular, these need to be defined. My interpretation of "Lake Store" would require you to be touching the water, but that is perhaps not what is intended. Level 11, "Lake Gate", and level 17, "Lake Speech" state distance is not a factor, but should be specific as to whether they can operate across different planes. "Lady of the Lake", other than one instance in Arthurian lore, has no reason for sexism as a spell for general use (although apparently there was reason in the home campaign). A "Lord of the Lake" makes as much sense, in the general case. Finally, the note on Call Blade spells states that "Each Lake may only yield one such blade at any time." Does this mean ever or for each caster? If it means ever, then the spell can be used preemptively to gather all the Lake Swords and deny them to anyone else. Perhaps there should be a limit of one blade per caster, so that you must return your blade to the lakes before summoning a new one?