It would be nice to be able to render tiles from features (vector data like Shape files) directly with a support for Cascading Stylesheets for defining the design in the style of:
http://mapnik-utils.googlecode.com/svn/trunk/serverside/cascadenik/doc/index.html
http://teczno.com/cascadenik-openstreetmap-II/
http://code.google.com/p/mapnik-utils/

It would be nice to have possibility to update existing tile tree (MapTiler tiles generated before) with new input raster and merge automatically new tiles into old tile tree – for example when merging map sheets or updating subset of existing trees. It would be useful also for merging input raster data with different coordinate systems.

GDAL2Tiles and MapTiles should support generation of the tiles in non-TMS directory structure...

The first candidate is OGC WMTS format (seems to be compatible with standard Google tile naming convension).

Second candidate are "Microsoft QuadTree" tiles known from MapCruncher for native Virtual Earth overlays (Spherical Mercator and QuadTree).

Third candidate are NASA World Wind tiles - so 512x512 Global Geodetic (-p geodetic) tiles with custom tile structure described at the site: http://issues.worldwind.arc.nasa.gov/confluence/download/attachments/394/world+wind+tile+systemt.gif

I summarized details to different tile naming convention for Spherical Mercator here:
http://www.maptiler.org/google-maps-coordinates-tile-bounds-projection/

Optimize MapTiler for generation of tiles on multi-core processors. Note: there is already a solution: http://help.maptiler.org/cluster

Rectification of images by specifying control points in the GUI would be nice (in the style of MapCruncher). Prototype of the GUI: http://oldmapsonline.googlecode.com/svn/trunk/georeference.html . Integration with the embedded web-server for local file preview and also WebKit in wxWidgets is necessary.

Embedding NeoQuant algorithm for RGBA from PNGNQ into GDAL library.

Support Amazon S3 as a storage for tiles: possible to reuse the code from tilecache.org project

Allow pixel precise warping for zoomed-in levels (those bigger then the native resolution of the input raster) – necessary for signal coverage maps for example.

OGC WMS access to the tiles - by generation of the mapfile with tileindexes for all tile levels - access to static tiles would be simple and very efficient with MapServer. Info: http://www.mapserver.org/

By a text specified on the command line. Possible also not-visible watermarks or info in the PNG headers.

use of Ozi's .MAP files for import georeference (by ozi2geotiff: http://ozi2geotiff.svn.sourceforge.net/viewvc/ozi2geotiff/trunk/ozi2geotiff.py?view=markup) and import of native OZF2/OZF3 files with help of ozf2img (now DeMapper: http://www.terraperfecta.com/demapper.php).

When clicking on the "Back" button in the GUI, some of the entered values are reset to their defaults. Most notably this is true for the title of the map, and the wanted zoom levels.

Perhaps check to se if user changed the defaults before resetting theese values?

In lieu of a GIS program and a base map to position a map one can use Google Earth to create an overlay. The result is quite acceptable.

It would then be nice to import the georeference directly from the KML file produced form Google Earth, rather than having to cut-and-paste from the KML file manually.

Warn in case there is a missing datum transformation (+towgs84 or +nadgrids) in the given definition of Spatial Reference Step in MapTiler GUI. Info: http://www.nabble.com/Re%3A-gdal-warp-code-silently-skipping-datum-shift-p3462229.html 

Generate optionaly also a viewer based on OpenZoom.org Flash Viewer for produced TMS tiles

Add Jpg compression level control.

Add 16bit per channel import/export for elevation sets (an 8 bit gray rgb image is no use)
eg 16bit grayscale tiff import & 16bit grayscale png output.

It would be nice to support any WMS server with a known projection (PROJ.4) like EPSG:4326 to be used as a source of rasters for generating tiles for mash-ups with specified area. Technically possible already with: http://www.gdal.org/frmt_wms.html

Implement unlimited zooming with existing rendered tiles - by resizing the tiles from the maximal available zoom by Google Maps API JavaScript on the client side.
It is possible to do this functionality by calling GGroundOverlay for tiles which are in the viewport.

Related links:
http://groups.google.com/group/Google-Maps-API/browse_thread/thread/b28081e9006eca3b/1a6fd39a9f2d369e?pli=1

The transition from Beta2 to released software is, in my oppinion, very much dependant on giving the user informative error messages.

I noticed the following two error messages when trying to give MapTiler an indexed PNG: Float expected, or index out of bounds. Only by really thinking through the problem was I able to discern that the PNG was suposed to bin in RGBA format, and processing/optimizing done only on the output of MapTiler.