Additions:

Open SSH compatiable SFTP added (improved speed and reliability).
SSH keygen added (advanced -> ssh)
Flash option for flash drives (cmd line -flash)
XCRC support added (adv -> transfers).
CCC (Clear Command Channel) support added.
PRET support added
No QUIT command option added
Scripting options for command line
Rubber banding of files, added
Decompression with password option added
Queue for decompression option added
AES/Winzip decompress support added
Color option for log added
PASV/Active command line options
SSH certificate drop down additions
GXS ICS format added (pro).
Put/get/recv/stor, list added to scripts/cmd settings
New Policy option - "don't save sessions on exit".
Skip Zero byte files transfer option added
SFTP site to site transfers.
SSL/TLS CA cert/key field added
New FTP proxy type: user@hostname proxyUser.
Winsock 1.1 option added.
Sorting of results in search tool added.
Multi-connection mode allows continued working during transfers.

Fixes/updates:

SSH key cache fixes
Compare/Sync not deleting empty dirs, fixed
Multiple connections bug fixed
Tabbing fixes
CCC failure problem fixed
Updated error reporting for notifications
Text invert for selected text in log
Multiple select for "total" option in properties
Upgraded to OpenSSL 0.9.8e
Decompression overwrite problems fixed
Rename issues for wildcards
Transfer mode from site profile override, fixed
Link verify bugs fixed
SSH/SFTP bugs in putty compatible packet size issues
Icon/Gui changes
Rename/overwrite problems on upload, fixed
SFTP connect/disconnect fixes
Permissions leak/crash problem fixed
PROT V/C fallback for return code 534 (pureftpd)
Mail message problem fixed
Command line not using remote startup folder, fixed
VMS cut/paste issues fixed
MVS rename issues fixed
Script/Cmd parsing fixes
Global proxy setting problems fixed
NAT/IP resolve fixes for PASV connections.
QUIT issued on exit for command line use.
NAT IP/Address resolves hostnames correctly.
GUI updates to queue (last col & speed).
Exiting Core FTP calls "QUIT" when connected.
Double clicking directory/file problem on some machines, fixed.
GUI crashing issues (mainly under 2003), fixed.
"Email after all transfers complete" - mail subject fixed
Shut down changed to 'Exit Core FTP'
Save options and fixes to last URL/Directory dropdown.
Global opton to save passwords in clear text (options -> policy).
PROT C/P fixes/updates.
Site to Site SFTP copying of permissions.
Search screen queue/download delays fixed.
MVS updates (chdir).
MVS HFS server type added (adv -> general -> server type).
SFTP updates (fixes/chmod/etc).
FXP connection fixes.
Putty compatible SFTP option (adv->ssh).
Directory interlocking (right click on file list, directory commands).
Repace ':' characters with '_' on downloaded files.
Offset hours able to use 0.5 increments.
File renaming updates to include full filenames, wildcards.
Memory leak on exit (search tool) fixed.

The 2.0 version contains major internal changes to increase speed and use memory more efficiently.