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Maybe you could give the option to upscale all boxes with pixel font pieces globally. If the dialoges are too small, the rest probably is as well. I guess monitors evolved since 2002. 

When zooming out on the overworld, there is sooooo much unused space there across all security levels... maybe you could put the modded maps over there.

Upload limits might be a good option for "hard mode". Hard mode could be as well to play through the game without being able to replay beaten levels to grind for credits. Stuff is quite costly here and having to decide for what to buy makes it quite hard to beat.

Excellent job! You're on a great way here to recreate this classic. A couple of suggestions:

The game lacks the navigation arrows at the edges of the map. As this is quite a mouse-dependant game, they would be quite helpful for navigation.

Font size is a difficult thing. My monitor is tiny at 1280x960, which is not enough for this kind of interface in fullscreen, as the font is too tiny. The map looks fine, but the pixel fonts would need to be upscaled 2x as it was done with the dialog system.

Speaking of which, I had the occurrence of a large block of text being too long, passing upwards and having the top part of it disappearing. Would be quite fitting to have a scrollbar in the chat-like interface as well.

Any plans of integrating modded levels in here? Maybe have a second campaign after the original story has been played through? Maybe some evil mod gang took over the internet after Disarrays defeat and S.M.A.R.T. has to do something about it?

Hm... gameplay could be really expanded in several ways, but that of course depends on your plans, as that might not fit a "remake", if you want to keep it like the classic. Bug should have 4 movement instead of 5 to be more balanced. Make the basic programs more useable through allowing only Level 1 programs in certain levels, which would even fit in the original game well, I'd say. Give them upload sizes (4 KB, 8 KB, 16 KB, 32 KB, 64 KB) and have each level have a certain amount of upload space for your programs. Have the decision between 1 Lv.2 program or 2 Lv.1 programs...

The option to "unload" programs to get faster through a round would fit the theme well.

Anyways, just some ideas. The game is a Flash classic by itself.