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Regarding the Mega Trainer 1.01/1.01a, Unlimited Mako Health, Unlimited He....

I like that the trainer let's you give your character extra skill points, but I wish it wouldn't give so much at once. I don't like having left over skill points once all my character skills are maxed out. I realize it's no big deal, but it just kind of bugs my OCD a little. Please, make a trainer that just gives you 1 or 2 extra skill points per activation. That way once all my characters skills are maxed I don't have a bunch of skill points left over I can't do anything with.

You can enter the cheat for more skill points manually. First, enable the console by going to Documents>BioWare>Mass Effect>Config on your computer. Then open BIOInput in Notepad. Find the line [Engine.Console] and under it add the line ConsoleKey=Tilde. Then when playing in game simply press the tilde key (above tab) to open the console, then type in the desired cheat.
Then just enter givetalentpoints #, replacing the # with any amount you want. this way you can boost certain talents and still leave some room for normal leveling up. For a full list of the cheats, go to gamefaqs.com.

I had the same problem, but I figured out a way around this.

First, max out your character's experience so that you reach the maximum level. This will make all the NPCs in your squad reach the same level. Use the console cheat to add experience, if you add 1,000,000 XP then you'll have maxed out.

Then, go to each character's development screen with the skill point trainer option OFF. Assign ONE (1) point to a skill, it doesn't matter which (I usually pick the class skill).

Now, switch to another character. Activate the skillpoint option. Note that the number of skillpoints available doesn't change immediately.

Switch back to the character you started with. Turn the skill point trainer option OFF. This character now has 99 points. Use the "auto assign" option. Bingo! Every skill is maxed, and there are no points left over. This is because a maxed out NPC in Mass Effect has exactly 100 points of skills.

This does not work for Shepherd, but that is no problem because you can use the console cheats to get as many skill points as you need.

Remember to turn the skill point trainer OFF after you have bumped the relevant character to 99 points, else you'll give everybody 99 points with no way to get rid of them. You may end up turning the option on and off once for each character; that's how I do it to make sure that I don't end up with unassigned skill points.