Hi Striker,
First of all, it's a pleasure to get feedback from maintainers, especially from hard workers like you and seeseekey

Even if features and bug fixes are slow to come, because some are really hard to reproduce and understand, and take time, I really want to say again that we're always willing to get feedback for Manaserv.
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* The projected Skill system is very limited, not permiting passive skills ( for example: A passive skill that permit the player be more stronger, or resist to some type of damage or magic, auras, etc ), and being only texts in a window ... ( Its very Important !)
* Please not attach the magic system only to runes and some equips ... its a MANA World ... not only mages with weak equips with runes can be users of magic ... please don´t ... ( Its very Important !)
* More options to Skills in mana-skills.xml, like : Description, usability, lua function, soundeffect, etc. Each level the skill increase some of their options (like hp healing, reduce the damage taken, etc ).
* Makes the mana-skills.xml have the possibility to a skill load a lua file

This issue is discussed
here, and seem to be adressed by Crush, who is the biggest warrior in this area.
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* The experience system without a base level its going to make a boring game, without the possibility to measure how strong and experienced its a player, the quests for a game like this its very affected. ( Calculating all skills to be a 'base experience' its not a good way to fix this ... ) ( Its very Important !)

The player has got a base level, so I don't really understand the point. Could you explain a bit?
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* Please, make the artists make the playerset your priority, this makes all remakes of equips later more easy ... ( Its very Important !)

Yes, that point is a pain in the ass. The playerset needs to be at least fixed when speaking of its orientation, or redone in a better way. Plus, we still need to separate the body into useful parts to help optimization and customization. Everything has been explained many times, but...
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* Makes each window can have different options for color, skin and measures.
* Please make a npc window more friendly, its simple boring to use it like its now.

Measures, why not. Color and skin are linked, I guess. Optimizations should be proposed point per point, but after a thorough discussion here on the forums. Like you're doing

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* Show in Status Window some stats like attack, magic attack, speed, ...
* Permit the stats to be configurable in ManaServ

Since attributes are soft coded (!), so are there derived stats, and so we need a flexible system for that. Some specification about a flexible system about this would be gladly welcome.
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* Permit the possibility to configure % of the gain of experience in ManaServ

A hard cap system is present in the system, for the soft capping system, ask Crush. Is that the kind of system you're searching for? (Capping is lowering the exp gained for too high level character, roughly said.)
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* When the mouse its up a skill, show a little description of the skill ( like showed items in inventory ).

Should be doable easily.

Others agreed about this?
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* Implement the 'usable' function of the items

Items can already be used through a script, as the apple is one example. Or did you mean something else by usable?
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* Put a close button in Npc Window

Adressed with issues #72 and #93 in the manasource.
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* Make more options to npc window, like text formating ( bold, italic, centralize, change color, etc )
* Made the possibility to add icons to npc window ( like add the items necessary to a quest )

A web based would be perfect. I, then, propose to wait for a QT port because the undertaking for Guichan would be quite big.
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* Make a Quest Log, and storing the main quests ids and descriptions in a xml file like quests.xml in manaserv/client.

The exact definition of the quest log is yet to be design, but in a perfect world, the client data shouldn't have any info about the quest log. Issue #145.
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* Not hardcode the dead messages

Indeed. Good point. Another xml file should maybe be designed?
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* Permit the mobs to use some type of skills ( for example, a mob that can use a teleport skill )

Your example is already a special case in that case.

Permitting to link skill with monsters shouldn't be hard, but she should focus on a well-made, documented and tested scriptable skill/special system first.
As for the bugs, I'd suggest you'd make issue for each one of them. and we'll try to adress them one after another.
(Don't forget to be precise about the steps to reproduce. Thanks

)
My best regards.