Hello,
Thank you all for your comments. I plan further development, so whatever you will find, I will at least try to solve.
@Jackos
You deserve special thanks. I don't wan't to defend myself but please remember I am still n00b if about programming

And I'd like to comment at least some of your cons:
90's looking UI - I fully agree. This is still on my "to-do" list. Honestly I have already tried to run the Sense SDK from eboelzner (on an early stage of the app) and I just couldn't get the controls to appear on the form. I haven't spent much time on it though as this was not the most important thing to do. And there are only a few controls in this app which are big enough to operate with finger
Poorly implemented AppToDate support - honestly I did it same way as you did for your ROMs

I know there is a possibility to download up-to-date cab directly from within the program, but I think the vital thing is to inform the user that something has changed. Nevertheless I will try to improve also here.
No way to backup e-mail accounts and signatures (I know it's difficult to assemble) - yes, you're right. And WiFi settings would also be fantastic to backup. I honestly don't know how to handle it. I did an extensive search among some developers forums and nothing up to now...
No file backup at all - this honestly was not in my plans. I use SettingsExporter in conjunction with PIMBackup in which I have my configuration (stored by the SettingsExporter by the way), and I backup all my files, contacts, messages and calendar within 2 clicks. I don't think any file backup is necessary...
No support for all registry types (not really needed though) - I've seen a tool written using NetCF where (according to the description) it is possible. I will ask the developer for help.
The rest of the "cons" concerns the configuration files which are subject to develop continously and independently on the tool itself. I was kinda hoping that this thread will grow with suggestions of other values of which I don't know and/or I don't use. So whatever you feel should be placed here, please post it

hence help to improve for other users.
HTC Touch Pro2
Best ROMs for Rhodium:
Jackos EVO WM6.5.x
Jackos S3 WM6.5
Currently on: Jackos S3 ManilaRUSH 1.7.1 PLK ## WM6.5 + Sense 2.5 + CHT 1.6.1
Radio: 4.49.25.91
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My contributions to the community: